ChemWiki - User contributions [en]

Mod:Hunt Research Group/calendar

2015-06-18T14:54:14Z

Vhc08:

Back to the main [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group wiki-page]
== Calendar ==

{| class="wikitable"
|-
! 1
! 2
! 3
! 4
|-
| Tricia (Done)
| Bryan Ward (Done)
| Claire Ashworth (Not Done)
| Precious Ugbomah (Not Done)
|-
| Vincent Chen (Done)
| Gabriel Lau (Not Done)
| Rebecca Rowe (Not Done)
| Ken Watson (Not Done)
|-
| Laila Bana (Not Done)
| Oliver Benton (Not Done)
| Christopher Sewell (Not Done)
| Chen Chen ( Not Done)
|-
| Aiswarya Prabha (Not Done)
|Ziyun Zhang (Done)
|Richard Fogarty (Not Done)
|Julie Schmauck ( Not Done )
|
|-
|-)
|}

<table border="1" cellpadding="5" width="1190">
<tr bgcolor="#66CCFF">
<th width="170px">Mon</th>
<th width="170px">Tues</th>
<th width="170px">Wed</th>
<th width="170px">Thur</th>
<th width="170px">Fri</th>
<th width="170px">Sat</th>
<th width="170px">Sun</th>
</tr>

<tr valign="top">
<td bgcolor="#4357CFF">'''1st June''' </td>
<td>2nd </td>
<td>3rd </td>
<td>4th </td>
<td>5th </td>
<td bgcolor="#33CC99">6th </td>
<td bgcolor="#33CC99">7th </td>
</tr>
<tr valign="top">
<td>8th </td>
<td>9th </td>
<td>10th </td>
<td>11th </td>
<td>12th </td>
<td bgcolor="#33CC99">13th </td>
<td bgcolor="#33CC99">14th </td>
</tr>
<tr valign="top">
<td>15th </td>
<td>16th </td>
<td>17th </td>
<td>18th </td>
<td>19th Bryan Away </td>
<td bgcolor="#33CC99">20th Bryan Away </td>
<td bgcolor="#33CC99">21st Bryan Away </td>
</tr>
<tr valign="top">
<td>22nd Bryan Away </td>
<td>23rd Bryan Away </td>
<td>24th Bryan Away </td>
<td>25th Bryan Away Richard F Exp </td>
<td>26th Bryan Away </td>
<td bgcolor="#33CC99">27th Bryan Away </td>
<td bgcolor="#33CC99">28th Bryan Away </td>
</tr>
<tr valign="top">
<td >29th Bryan Away </td>
<td>30th </td>
<td bgcolor="#4357CFF">'''1st July''' </td>
<td>2nd </td>
<td>3rd Tricia Away </td>
<td bgcolor="#33CC99">4th Tricia Away </td>
<td bgcolor="#33CC99">5th Tricia Away </td>
</tr>
<tr valign="top">
<td >6th Tricia Away </td>
<td>7th Richard F Exp </td>
<td>8th Richard F Exp </td>
<td>9th Richard F Exp </td>
<td>10th Richard F Exp </td>
<td bgcolor="#33CC99">11th </td>
<td bgcolor="#33CC99">12th </td>
</tr>
<tr valign="top">
<td>13th Richard F Away</td>
<td>14th </td>
<td>15th </td>
<td>16th </td>
<td>17th </td>
<td bgcolor="#33CC99">18th </td>
<td bgcolor="#33CC99">19th </td>
</tr>
<tr valign="top">
<td>20th </td>
<td>21st </td>
<td>22nd </td>
<td>23rd </td>
<td>24th </td>
<td bgcolor="#33CC99">25th </td>
<td bgcolor="#33CC99">26th </td>
</tr>
<tr valign="top">
<td>27th </td>
<td>28th </td>
<td>29th Tricia Away </td>
<td>30th Tricia Away </td>
<td>31st Tricia Away </td>
<td bgcolor="#4357CFF">'''1st August''' Tricia Away </td>
<td bgcolor="#33CC99">2nd Tricia Away </td>
</tr>
<tr valign="top">
<td>3rd Tricia Away Richard F Away </td>
<td>4th Tricia Away Richard F Away </td>
<td>5th Tricia Away Richard F Away </td>
<td>6th Tricia Away Richard F Away </td>
<td>7th Tricia Away Richard F Away </td>
<td bgcolor="#33CC99">8th Tricia Away </td>
<td bgcolor="#33CC99">9th Tricia Away </td>
</tr>
<tr valign="top">
<td>10th Tricia Away Richard F Away </td>
<td>11th Tricia Away Richard F Away </td>
<td>12th Tricia Away </td>
<td>13th Tricia Away </td>
<td>14th Tricia Away </td>
<td bgcolor="#33CC99">15th Tricia Away </td>
<td bgcolor="#33CC99">16th Tricia Away </td>
</tr>
<tr valign="top">
<td>17th </td>
<td>18th </td>
<td>19th </td>
<td>20th </td>
<td>21st </td>
<td bgcolor="#33CC99">22nd </td>
<td bgcolor="#33CC99">23rd </td>
</tr>
<tr valign="top">
<td>24th </td>
<td>25th </td>
<td>26th </td>
<td>27th </td>
<td>28th </td>
<td bgcolor="#33CC99">29th </td>
<td bgcolor="#33CC99">30th </td>
</tr>
<tr valign="top">
<td>31st </td>
<td bgcolor="#4357CFF">'''1st September''' </td>
<td>2nd </td>
<td>3rd </td>
<td>4th </td>
<td bgcolor="#33CC99">5th </td>
<td bgcolor="#33CC99">6th </td>
</tr>
<tr valign="top">
<td>7th </td>
<td>8th </td>
<td>9th </td>
<td>10th </td>
<td>11th </td>
<td bgcolor="#33CC99">12th Tricia Away </td>
<td bgcolor="#33CC99">13th Tricia Away </td>
</tr>
<tr valign="top">
<td>14th Tricia Away </td>
<td>15th Tricia Away </td>
<td>16th Tricia Away </td>
<td>17th Tricia Away </td>
<td>18th Tricia Away </td>
<td bgcolor="#33CC99">19th Tricia Away </td>
<td bgcolor="#33CC99">20th Tricia Away </td>
</tr>
<tr valign="top">
<td>21st </td>
<td>22nd </td>
<td>23rd </td>
<td>24th </td>
<td>25th </td>
<td bgcolor="#33CC99">26th </td>
<td bgcolor="#33CC99">27th </td>
</tr>
<tr valign="top">
<td>28th </td>
<td>29th </td>
<td>30th </td>
<td bgcolor="#4357CFF">'''1st October''' </td>
<td>2nd </td>
<td bgcolor="#33CC99">3rd </td>
<td bgcolor="#33CC99">4th </td>
</tr>
</table>

Mod:Hunt Research Group/calendar

2015-04-01T10:18:57Z

Vhc08:

Mod:Hunt Research Group/calendar

2015-04-01T10:18:23Z

Vhc08:

Mod:Hunt Research Group/calendar

2014-12-16T09:51:05Z

Vhc08:

Back to the main [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group wiki-page]
== Calendar ==

{| class="wikitable"
|-
! 1
! 2
! 3
! 4
|-
| Tricia (Done)
| Matthew Clough (Not Done)
| Bryan Ward (Done)
| Claire Ashworth (Done)
|-
| Precious Ugbomah (Done)
| Richard Matthews (Done)
| Vincent Chen (Done)
| Gabriel Lau (Not Done)
|-
| Rebecca Rowe (Not Done)
| Patricia Ho (Done)
| Ken Watson (Done)
| Laila Bana (Not Done)
|-
| Oliver Benton (Not Done)
|Christopher Sewell (Not Done)
|Chen Chen (Not Done)
|Aiswarya Prabha (Not Done)
|-
|-)
|}

<table border="1" cellpadding="5" width="1190">
<tr bgcolor="#66CCFF">
<th width="170px">Mon</th>
<th width="170px">Tues</th>
<th width="170px">Wed</th>
<th width="170px">Thur</th>
<th width="170px">Fri</th>
<th width="170px" bgcolor="#CCCCCC">Sat</th>
<th width="170px" bgcolor="#CCCCCC">Sun</th>
</tr>
<tr valign="top">
<td bgcolor="#4357CFF">'''1st December''' </td>
<td>2nd </td>
<td>3rd </td>
<td>4th </td>
<td>5th </td>
<td bgcolor="#CCCCCC">6th </td>
<td bgcolor="#CCCCCC">7th </td>
</tr>
<tr valign="top">
<td>8th Richard F Away </td>
<td>9th Richard F Away </td>
<td>10th Richard F Away </td>
<td>11th Richard F Away </td>
<td>12th </td>
<td bgcolor="#CCCCCC">13th </td>
<td bgcolor="#CCCCCC">14th </td>
</tr>
<tr valign="top">
<td>15th Richard M Away </td>
<td>16th Richard F Away Richard M Away </td>
<td>17th Richard F Away Richard M Away </td>
<td>18th </td>
<td bgcolor="#FFFF00">19th '''END OF TERM''' Bryan Away Precious Away </td>
<td bgcolor="#CCCCCC">20th </td>
<td bgcolor="#CCCCCC">21st </td>
</tr>
<tr valign="top">
<td>22nd Tricia Away Ken Away Bryan Away Precious Away Richard M Away </td>
<td>23rd Tricia Away Ken Away Claire Away Precious Away Richard M Away </td>
<td bgcolor="#33CC99">24th '''College closed'''</td>
<td bgcolor="#33CC99">25th '''College closed'''</td>
<td bgcolor="#33CC99">26th '''College closed'''</td>
<td bgcolor="#CCCCCC">27th </td>
<td bgcolor="#CCCCCC">28th </td>
</tr>
<tr valign="top">
<td bgcolor="#33CC99">29th '''College closed'''</td>
<td bgcolor="#33CC99">30th '''College closed'''</td>
<td bgcolor="#33CC99">31st '''College closed'''</td>
<td bgcolor="#4357CFF">'''1st January 2015''' '''College closed'''</td>
<td bgcolor="#33CC99">2nd '''College closed'''</td>
<td bgcolor="#CCCCCC">3rd </td>
<td bgcolor="#CCCCCC">4th </td>
<tr valign="top">
<td>5th Precious Away </td>
<td>6th </td>
<td>7th </td>
<td>8th </td>
<td>9th </td>
<td bgcolor="#CCCCCC">10th </td>
<td bgcolor="#CCCCCC">11th </td>
</tr>
<tr valign="top">
<td bgcolor="#FFFF00">12th '''NEW TERM'''</td>
<td>13th </td>
<td>14th </td>
<td>15th </td>
<td>16th </td>
<td bgcolor="#CCCCCC">17th </td>
<td bgcolor="#CCCCCC">18th </td>
</tr>
<tr valign="top">
<td>19th </td>
<td>20th </td>
<td>21st </td>
<td>22nd </td>
<td>23rd </td>
<td bgcolor="#CCCCCC">24th </td>
<td bgcolor="#CCCCCC">25th </td>
</tr>
<tr valign="top">
<td>26th </td>
<td>27th </td>
<td>28th </td>
<td>29th </td>
<td>30th </td>
<td bgcolor="#CCCCCC">31st </td>
<td bgcolor="#4357CFF">'''1st February 2015''' </td>
</tr>
</table>

Mod:Hunt Research Group/calendar

2014-07-15T10:14:45Z

Vhc08:

== Calendar ==

*Tricia (Not Done)
*Abdihakim Hassan (Not Done)
*Bryan Ward (Not Done)
*Claire Ashworth (Not Done)
*Matthew Clough (Done)
*Precious Ugbomah (Not Done)
*Richard Matthews (Not Done)
*Vincent Chen (Not Done)
*Gabriel Lau (Not Done)
*Rebecca Rowe (Not Done)
*Patricia Ho (Done)
*Giacomo Damilano (Not Done)
*Richard Fogarty (Not Done)

<table border="1" cellpadding="5" width="1190">
<tr bgcolor="#66CCFF">
<th width="170px">Mon</th>
<th width="170px">Tues</th>
<th width="170px">Wed</th>
<th width="170px">Thur</th>
<th width="170px">Fri</th>
<th width="170px" bgcolor="#CCCCCC">Sat</th>
<th width="170px" bgcolor="#CCCCCC">Sun</th>
<tr valign="top">
<td bgcolor="#339933">26th '''College closed''' '''Bank holiday'''</td>
<td >27th </td>
<td>28th </td>
<td>29th </td>
<td>30th (Giacomo Away)</td>
<td bgcolor="#CCCCCC">31st </td>
<td bgcolor="#4357CFF">1st June (Giacomo Away) </td>
</tr>
<tr valign="top">
<td>2nd (Giacomo Away)</td>
<td>3rd '''(Richard F - paper)''' (Giacomo Away)</td>
<td>4th CECAM workshop Claire away (Giacomo Away) (Patricia away)</td>
<td>5th CECAM workshop Claire away (Patricia away) (Giacomo Away) (Richard F away)</td>
<td>6th CECAM workshop Claire away (Patricia away)</td>
<td bgcolor="#CCCCCC">7th </td>
<td bgcolor="#CCCCCC">8th </td>
</tr>
<tr valign="top">
<td>9th </td>
<td>10th '''(Matt - paper)'''</td>
<td>11th </td>
<td>12th </td>
<td>13th </td>
<td bgcolor="#CCCCCC">14th </td>
<td bgcolor="#CCCCCC">15th </td>
</tr>
<tr valign="top">
<td>16th LIBLICE conference-Gabriel </td>
<td>17th '''(Hakim-presentation practice)''' LIBLICE conference-Gabriel </td>
<td>18th LIBLICE conference-Gabriel </td>
<td>19th LIBLICE conference-Gabriel </td>
<td>20th LIBLICE conference-Gabriel </td>
<td bgcolor="#CCCCCC">21st </td>
<td bgcolor="#CCCCCC">22nd </td>
</tr>
<tr valign="top">
<td>23rd </td>
<td>24th </td>
<td>25th </td>
<td>26th '''(Talk practice)'''</td>
<td bgcolor="#FFA500">27th '''End of term''' Richard F away</td>
<td bgcolor="#CCCCCC">28th </td>
<td bgcolor="#CCCCCC">29th </td>
</tr>
<tr valign="top">
<td>30th (Richard F away)</td>
<td bgcolor="#4357CFF" >1st July {{fontcolor|#FFD700|'''PhD Symposium (Chem.)'''}} (Richard F away)</td>
<td>2nd (Richard F away)</td>
<td>3rd </td>
<td>4th </td>
<td bgcolor="#CCCCCC">5th </td>
<td bgcolor="#CCCCCC">6th EUCHEM-Richard & Claire</td>
</tr>
<tr valign="top">
<td>7th Bryan Away EUCHEM-Richard&Claire</td>
<td>8th Bryan Away EUCHEM-Richard & Claire</td>
<td>9th Bryan Away EUCHEM-Richard & Claire</td>
<td>10th Bryan Away EUCHEM-Richard & Claire</td>
<td>11th Bryan Away EUCHEM-Richard & Claire</td>
<td bgcolor="#CCCCCC">12th </td>
<td bgcolor="#CCCCCC">13th </td>
</tr>
<tr valign="top">
<td>14th Bryan Away Richard away Claire away</td>
<td>15th Bryan Away Richard away Claire away</td>
<td>16th Bryan Away Richard away Claire away Vincent away</td>
<td>17th Bryan Away Richard away Matthew Away Claire away Vincent away</td>
<td>18th Bryan Away Richard away Claire away</td>
<td bgcolor="#CCCCCC">19th </td>
<td bgcolor="#CCCCCC">20th </td>
</tr>
<tr valign="top">
<td>21st Liquid Matter-Gabriel Vincent away</td>
<td>22nd Liquid Matter-Gabriel</td>
<td>23rd Gaussian workshop - Claire & Bryan Liquid Matter-Gabriel</td>
<td>24th Gaussian workshop - Claire & Bryan Liquid Matter-Gabriel </td>
<td>25th Liquid Matter-Gabriel </td>
<td bgcolor="#CCCCCC">26th </td>
<td bgcolor="#CCCCCC">27th </td>
</tr>
<tr valign="top">
<td>28th Matthew Away </td>
<td>29th Matthew Away </td>
<td>30th Matthew Away </td>
<td>31st Bryan Away Matthew Away </td>
<td bgcolor="#4357CFF">1st August Bryan Away Matthew Away </td>
<td bgcolor="#CCCCCC">2nd </td>
<td bgcolor="#CCCCCC">3rd </td>
</tr>
<tr valign="top">
<td>4th Bryan on hiatus Matthew Away </td>
<td>5th Bryan on hiatus Matthew Away </td>
<td>6th Bryan on hiatus Matthew Away </td>
<td>7th Bryan on hiatus Matthew Away </td>
<td>8th Bryan on hiatus Matthew Away </td>
<td bgcolor="#CCCCCC">9th </td>
<td bgcolor="#CCCCCC">10th </td>
</tr>
<tr valign="top">
<td>11th Bryan on hiatus Matthew Away </td>
<td>12th Bryan on hiatus </td>
<td>13th Bryan on hiatus </td>
<td>14th Bryan on hiatus </td>
<td>15th Bryan on hiatus </td>
<td bgcolor="#CCCCCC">16th </td>
<td bgcolor="#CCCCCC">17th </td>
</tr>
<tr valign="top">
<td>18th Bryan on hiatus </td>
<td>19th Bryan on hiatus </td>
<td>20th Bryan on hiatus </td>
<td>21st Bryan on hiatus </td>
<td>22nd Bryan on hiatus </td>
<td bgcolor="#CCCCCC">23rd </td>
<td bgcolor="#CCCCCC">24th </td>
</tr>
<tr valign="top">
<td bgcolor="#339933">25th '''College closed''' '''Bank holiday'''</td>
<td>26th Bryan on hiatus </td>
<td>27th Bryan on hiatus </td>
<td>28th Bryan on hiatus </td>
<td>39th Bryan on hiatus </td>
<td bgcolor="#CCCCCC">30th </td>
<td bgcolor="#CCCCCC">31st </td>
</tr>
<tr valign="top">
<td bgcolor="#4357CFF">1st September Bryan on hiatus </td>
<td>2nd Bryan on hiatus </td>
<td>3rd Bryan on hiatus </td>
<td>4th Bryan on hiatus </td>
<td>5th Bryan on hiatus </td>
<td bgcolor="#CCCCCC">6th </td>
<td bgcolor="#CCCCCC">7th </td>
</tr>
<tr valign="top">
<td>8th </td>
<td>9th </td>
<td>10th </td>
<td>11th </td>
<td>12th </td>
<td bgcolor="#CCCCCC">13th </td>
<td bgcolor="#CCCCCC">14th </td>
</tr>
<tr valign="top">
<td>15th </td>
<td>16th </td>
<td>17th </td>
<td>18th </td>
<td>19th </td>
<td bgcolor="#CCCCCC">20th </td>
<td bgcolor="#CCCCCC">21st </td>
</tr>
<tr valign="top">
<td>22nd </td>
<td>23rd </td>
<td>24th </td>
<td>25th </td>
<td>26th </td>
<td bgcolor="#CCCCCC">27th </td>
<td bgcolor="#CCCCCC">28th </td>
</tr>
<tr valign="top">
<td>29th </td>
<td>30th </td>
<td bgcolor="#4357CFF">1st October </td>
<td> </td>
<td> </td>
<td bgcolor="#CCCCCC"> </td>
<td bgcolor="#CCCCCC"> </td>
</tr>
</table>

Mod:Hunt Research Group/calendar

2014-07-10T10:02:35Z

Vhc08:

== Calendar ==

*Tricia (Not Done)
*Abdihakim Hassan (Not Done)
*Bryan Ward (Not Done)
*Claire Ashworth (Not Done)
*Matthew Clough (Done)
*Precious Ugbomah (Not Done)
*Richard Matthews (Not Done)
*Vincent Chen (Not Done)
*Gabriel Lau (Not Done)
*Rebecca Rowe (Not Done)
*Patricia Ho (Done)
*Giacomo Damilano (Not Done)
*Richard Fogarty (Not Done)

<table border="1" cellpadding="5" width="1190">
<tr bgcolor="#66CCFF">
<th width="170px">Mon</th>
<th width="170px">Tues</th>
<th width="170px">Wed</th>
<th width="170px">Thur</th>
<th width="170px">Fri</th>
<th width="170px" bgcolor="#CCCCCC">Sat</th>
<th width="170px" bgcolor="#CCCCCC">Sun</th>
<tr valign="top">
<td bgcolor="#339933">26th '''College closed''' '''Bank holiday'''</td>
<td >27th </td>
<td>28th </td>
<td>29th </td>
<td>30th (Giacomo Away)</td>
<td bgcolor="#CCCCCC">31st </td>
<td bgcolor="#4357CFF">1st June (Giacomo Away) </td>
</tr>
<tr valign="top">
<td>2nd (Giacomo Away)</td>
<td>3rd '''(Richard F - paper)''' (Giacomo Away)</td>
<td>4th CECAM workshop Claire away (Giacomo Away) (Patricia away)</td>
<td>5th CECAM workshop Claire away (Patricia away) (Giacomo Away) (Richard F away)</td>
<td>6th CECAM workshop Claire away (Patricia away)</td>
<td bgcolor="#CCCCCC">7th </td>
<td bgcolor="#CCCCCC">8th </td>
</tr>
<tr valign="top">
<td>9th </td>
<td>10th '''(Matt - paper)'''</td>
<td>11th </td>
<td>12th </td>
<td>13th </td>
<td bgcolor="#CCCCCC">14th </td>
<td bgcolor="#CCCCCC">15th </td>
</tr>
<tr valign="top">
<td>16th LIBLICE conference-Gabriel </td>
<td>17th '''(Hakim-presentation practice)''' LIBLICE conference-Gabriel </td>
<td>18th LIBLICE conference-Gabriel </td>
<td>19th LIBLICE conference-Gabriel </td>
<td>20th LIBLICE conference-Gabriel </td>
<td bgcolor="#CCCCCC">21st </td>
<td bgcolor="#CCCCCC">22nd </td>
</tr>
<tr valign="top">
<td>23rd </td>
<td>24th </td>
<td>25th </td>
<td>26th '''(Talk practice)'''</td>
<td bgcolor="#FFA500">27th '''End of term''' Richard F away</td>
<td bgcolor="#CCCCCC">28th </td>
<td bgcolor="#CCCCCC">29th </td>
</tr>
<tr valign="top">
<td>30th (Richard F away)</td>
<td bgcolor="#4357CFF" >1st July {{fontcolor|#FFD700|'''PhD Symposium (Chem.)'''}} (Richard F away)</td>
<td>2nd (Richard F away)</td>
<td>3rd </td>
<td>4th </td>
<td bgcolor="#CCCCCC">5th </td>
<td bgcolor="#CCCCCC">6th EUCHEM-Richard & Claire</td>
</tr>
<tr valign="top">
<td>7th Bryan Away EUCHEM-Richard&Claire</td>
<td>8th Bryan Away EUCHEM-Richard & Claire</td>
<td>9th Bryan Away EUCHEM-Richard & Claire</td>
<td>10th Bryan Away EUCHEM-Richard & Claire</td>
<td>11th Bryan Away EUCHEM-Richard & Claire</td>
<td bgcolor="#CCCCCC">12th </td>
<td bgcolor="#CCCCCC">13th </td>
</tr>
<tr valign="top">
<td>14th Bryan Away Richard away Claire away</td>
<td>15th Bryan Away Richard away Claire away</td>
<td>16th Bryan Away Richard away Claire away Vincent away</td>
<td>17th Bryan Away Richard away Matthew Away Claire away Vincent away</td>
<td>18th Bryan Away Richard away Claire away</td>
<td bgcolor="#CCCCCC">19th </td>
<td bgcolor="#CCCCCC">20th </td>
</tr>
<tr valign="top">
<td>21st Liquid Matter-Gabriel</td>
<td>22nd Liquid Matter-Gabriel</td>
<td>23rd Gaussian workshop - Claire & Bryan Liquid Matter-Gabriel</td>
<td>24th Gaussian workshop - Claire & Bryan Liquid Matter-Gabriel </td>
<td>25th Liquid Matter-Gabriel </td>
<td bgcolor="#CCCCCC">26th </td>
<td bgcolor="#CCCCCC">27th </td>
</tr>
<tr valign="top">
<td>28th Matthew Away </td>
<td>29th Matthew Away </td>
<td>30th Matthew Away </td>
<td>31st Bryan Away Matthew Away </td>
<td bgcolor="#4357CFF">1st August Bryan Away Matthew Away </td>
<td bgcolor="#CCCCCC">2nd </td>
<td bgcolor="#CCCCCC">3rd </td>
</tr>
<tr valign="top">
<td>4th Bryan on hiatus Matthew Away </td>
<td>5th Bryan on hiatus Matthew Away </td>
<td>6th Bryan on hiatus Matthew Away </td>
<td>7th Bryan on hiatus Matthew Away </td>
<td>8th Bryan on hiatus Matthew Away </td>
<td bgcolor="#CCCCCC">9th </td>
<td bgcolor="#CCCCCC">10th </td>
</tr>
<tr valign="top">
<td>11th Bryan on hiatus Matthew Away </td>
<td>12th Bryan on hiatus </td>
<td>13th Bryan on hiatus </td>
<td>14th Bryan on hiatus </td>
<td>15th Bryan on hiatus </td>
<td bgcolor="#CCCCCC">16th </td>
<td bgcolor="#CCCCCC">17th </td>
</tr>
<tr valign="top">
<td>18th Bryan on hiatus </td>
<td>19th Bryan on hiatus </td>
<td>20th Bryan on hiatus </td>
<td>21st Bryan on hiatus </td>
<td>22nd Bryan on hiatus </td>
<td bgcolor="#CCCCCC">23rd </td>
<td bgcolor="#CCCCCC">24th </td>
</tr>
<tr valign="top">
<td bgcolor="#339933">25th '''College closed''' '''Bank holiday'''</td>
<td>26th Bryan on hiatus </td>
<td>27th Bryan on hiatus </td>
<td>28th Bryan on hiatus </td>
<td>39th Bryan on hiatus </td>
<td bgcolor="#CCCCCC">30th </td>
<td bgcolor="#CCCCCC">31st </td>
</tr>
<tr valign="top">
<td bgcolor="#4357CFF">1st September Bryan on hiatus </td>
<td>2nd Bryan on hiatus </td>
<td>3rd Bryan on hiatus </td>
<td>4th Bryan on hiatus </td>
<td>5th Bryan on hiatus </td>
<td bgcolor="#CCCCCC">6th </td>
<td bgcolor="#CCCCCC">7th </td>
</tr>
<tr valign="top">
<td>8th </td>
<td>9th </td>
<td>10th </td>
<td>11th </td>
<td>12th </td>
<td bgcolor="#CCCCCC">13th </td>
<td bgcolor="#CCCCCC">14th </td>
</tr>
<tr valign="top">
<td>15th </td>
<td>16th </td>
<td>17th </td>
<td>18th </td>
<td>19th </td>
<td bgcolor="#CCCCCC">20th </td>
<td bgcolor="#CCCCCC">21st </td>
</tr>
<tr valign="top">
<td>22nd </td>
<td>23rd </td>
<td>24th </td>
<td>25th </td>
<td>26th </td>
<td bgcolor="#CCCCCC">27th </td>
<td bgcolor="#CCCCCC">28th </td>
</tr>
<tr valign="top">
<td>29th </td>
<td>30th </td>
<td bgcolor="#4357CFF">1st October </td>
<td> </td>
<td> </td>
<td bgcolor="#CCCCCC"> </td>
<td bgcolor="#CCCCCC"> </td>
</tr>
</table>

Mod:Hunt Research Group/calendar

2014-04-08T13:50:04Z

Vhc08:

== Calendar ==

*Tricia (Done)
*Abdihakim Hassan (Done)
*Bryan Ward (Done)
*Claire Ashworth (Done)
*Matthew Clough (Done)
*Precious Ugbomah (Done)
*Richard Matthews (Done)
*Vincent Chen (Done)
*Gabriel Lau (Done)
*Rebecca Rowe (Done)
*Patricia Ho (Not Done)
*Giacomo Damilano (Done)

<table border="1" cellpadding="5" width="1190">
<tr bgcolor="#66CCFF">
<th width="170px">Mon</th>
<th width="170px">Tues</th>
<th width="170px">Wed</th>
<th width="170px">Thur</th>
<th width="170px">Fri</th>
<th width="170px" bgcolor="#CCCCCC">Sat</th>
<th width="170px" bgcolor="#CCCCCC">Sun</th>
<tr valign="top">
<td> </td>
<td> </td>
<td> </td>
<td> </td>
<td> </td>
<td bgcolor="#4357CFF">1st March </td>
<td bgcolor="#CCCCCC">2nd </td>
</tr>
<tr valign="top">
<td>3rd Richard away </td>
<td>4th '''(Vincent)''' Richard away </td>
<td>5th Richard away Vincent away </td>
<td>6th Richard away </td>
<td>7th Richard away </td>
<td bgcolor="#CCCCCC">8th </td>
<td bgcolor="#CCCCCC">9th </td>
</tr>
<tr valign="top">
<td>10th Richard away </td>
<td>11th '''(Becky)''' Richard away </td>
<td>12th Richard away </td>
<td>13th Richard away </td>
<td>14th Richard away </td>
<td bgcolor="#CCCCCC">15th </td>
<td bgcolor="#CCCCCC">16th </td>
</tr>
<tr valign="top">
<td>17th </td>
<td>18th '''(Giacomo)''' Richard postdoc workshop</td>
<td>19th </td>
<td>20th </td>
<td>21st Claire away</td>
<td bgcolor="#CCCCCC">22nd </td>
<td bgcolor="#CCCCCC">23rd </td>
</tr>
<tr valign="top">
<td>24th </td>
<td>25th '''(Patricia)'''</td>
<td>26th </td>
<td>27th </td>
<td bgcolor="#FFA500">28th '''End of term'''</td>
<td bgcolor="#CCCCCC">29th </td>
<td bgcolor="#CCCCCC">30th </td>
</tr>
<tr valign="top">
<td>31st Becky away rowing </td>
<td bgcolor="#4357CFF">1st April '''(Precious)''' DL_Poly workshop - Claire, Richard</td>
<td>2nd DL_Poly workshop - Claire, Richard Becky away rowing </td>
<td>3rd Becky away rowing </td>
<td>4th Becky away rowing </td>
<td bgcolor="#CCCCCC">5th Becky away rowing </td>
<td bgcolor="#CCCCCC">6th Becky away rowing </td>
</tr>
<tr valign="top">
<td>7th Becky away rowing </td>
<td >8th '''(Matthew)''' Becky away rowing ADF workshop - Vincent, Tricia</td>
<td>9th Matthew Away Becky away rowing ADF workshop - Vincent, Tricia</td>
<td>10th Matthew Away Vincent in Daresbury</td>
<td>11th Matthew Away </td>
<td bgcolor="#CCCCCC">12th </td>
<td bgcolor="#CCCCCC">13th </td>
</tr>
<tr valign="top">
<td>14th Bryan Away </td>
<td >15th Bryan Away '''(Group activity)'''</td>
<td>16th Tricia away Giacomo away </td>
<td bgcolor="#339933">17th '''College Closed'''</td>
<td bgcolor="#339933">18th '''College Closed'''</td>
<td bgcolor="#CCCCCC">19th '''College Closed'''</td>
<td bgcolor="#CCCCCC">20th '''College Closed'''</td>
</tr>
<tr valign="top">
<td bgcolor="#339933">21st '''College Closed'''</td>
<td bgcolor="#339933" >22nd '''College Closed'''</td>
<td>23rd Tricia away Richard away Precious away Giacomo away Gabriel away </td>
<td>24th Richard away Giacomo away Gabriel away Precious away </td>
<td>25th Richard away Giacomo away Gabriel away </td>
<td bgcolor="#FFA500">26th '''Start of term''' Giacomo away </td>
<td bgcolor="#CCCCCC">27th Giacomo away </td>
</tr>
<tr valign="top">
<td>28th Giacomo away </td>
<td >29th </td>
<td>30th </td>
<td bgcolor="#4357CFF">1st May </td>
<td>2nd </td>
<td bgcolor="#CCCCCC">3rd </td>
<td bgcolor="#CCCCCC">4th </td>
</tr>
<tr valign="top">
<td bgcolor="#339933">5th '''College Closed''' '''Bank holiday'''</td>
<td >6th '''(Tricia-DFT functionals)'''</td>
<td>7th </td>
<td>8th </td>
<td>9th </td>
<td bgcolor="#CCCCCC">10th </td>
<td bgcolor="#CCCCCC">11th </td>
</tr>
<tr valign="top">
<td >12th </td>
<td >13th </td>
<td>14th </td>
<td>15th </td>
<td>16th </td>
<td bgcolor="#CCCCCC">17th </td>
<td bgcolor="#CCCCCC">18th </td>
</tr>
<tr valign="top">
<td >19th Careers course - Vincent, Gabriel</td>
<td >20th Careers course - Vincent, Gabriel</td>
<td>21st Careers course - Vincent, Gabriel</td>
<td>22nd </td>
<td>23rd </td>
<td bgcolor="#CCCCCC">24th </td>
<td bgcolor="#CCCCCC">25th </td>
</tr>
<tr valign="top">
<td bgcolor="#339933">26th '''College closed''' '''Bank holiday'''</td>
<td >27th </td>
<td>28th </td>
<td>29th </td>
<td>30th </td>
<td bgcolor="#CCCCCC">31st </td>
<td bgcolor="#4357CFF">1st June </td>
</tr>
<tr valign="top">
<td>2nd </td>
<td>3rd </td>
<td>4th CECAM workshop</td>
<td>5th CECAM workshop Claire away</td>
<td>6th CECAM workshop Claire away</td>
<td bgcolor="#CCCCCC">7th </td>
<td bgcolor="#CCCCCC">8th </td>
</tr>
<tr valign="top">
<td>9th </td>
<td>10th </td>
<td>11th </td>
<td>12th </td>
<td>13th </td>
<td bgcolor="#CCCCCC">14th </td>
<td bgcolor="#CCCCCC">15th </td>
</tr>
<tr valign="top">
<td>16th </td>
<td>17th </td>
<td>18th </td>
<td>19th </td>
<td>20th </td>
<td bgcolor="#CCCCCC">21st </td>
<td bgcolor="#CCCCCC">22nd </td>
</tr>
<tr valign="top">
<td>23rd </td>
<td>24th </td>
<td>25th </td>
<td>26th </td>
<td bgcolor="#FFA500">27th '''End of term'''</td>
<td bgcolor="#CCCCCC">28th </td>
<td bgcolor="#CCCCCC">29th </td>
</tr>
<tr valign="top">
<td>30th </td>
<td bgcolor="#4357CFF" >1st July {{fontcolor|#FFD700|'''PhD Symposium (Chem.)'''}}</td>
<td>2nd </td>
<td>3rd </td>
<td>4th </td>
<td bgcolor="#CCCCCC">5th </td>
<td bgcolor="#CCCCCC">6th EUCHEM</td>
</tr>
<tr valign="top">
<td>7th EUCHEM</td>
<td>8th EUCHEM</td>
<td>9th EUCHEM</td>
<td>10th EUCHEM</td>
<td>11th EUCHEM</td>
<td bgcolor="#CCCCCC">12th </td>
<td bgcolor="#CCCCCC">13th </td>
</tr>
<tr valign="top">
<td>14th Richard away</td>
<td>15th Richard away</td>
<td>16th Richard away</td>
<td>17th Richard away</td>
<td>18th Richard away</td>
<td bgcolor="#CCCCCC">19th </td>
<td bgcolor="#CCCCCC">20th </td>
</tr>
<tr valign="top">
<td>21st </td>
<td>22nd </td>
<td>23rd Gaussian workshop - Claire</td>
<td>24th Gaussian workshop - Claire</td>
<td>25th </td>
<td bgcolor="#CCCCCC">26th </td>
<td bgcolor="#CCCCCC">27th </td>
</tr>

<tr valign="top">
<td>28th </td>
<td>29th </td>
<td>30th </td>
<td>31st </td>
<td bgcolor="#4357CFF">1st August </td>
<td bgcolor="#CCCCCC">2nd </td>
<td bgcolor="#CCCCCC">3rd </td>
</tr>
</table>

Mod:Hunt Research Group/calendar

2014-04-08T13:47:58Z

Vhc08:

== Calendar ==

*Tricia (Done)
*Abdihakim Hassan (Done)
*Bryan Ward (Done)
*Claire Ashworth (Done)
*Matthew Clough (Done)
*Precious Ugbomah (Done)
*Richard Matthews (Done)
*Vincent Chen (Done)
*Gabriel Lau (Done)
*Rebecca Rowe (Done)
*Patricia Ho (Not Done)
*Giacomo Damilano (Done)

<table border="1" cellpadding="5" width="1190">
<tr bgcolor="#66CCFF">
<th width="170px">Mon</th>
<th width="170px">Tues</th>
<th width="170px">Wed</th>
<th width="170px">Thur</th>
<th width="170px">Fri</th>
<th width="170px" bgcolor="#CCCCCC">Sat</th>
<th width="170px" bgcolor="#CCCCCC">Sun</th>
<tr valign="top">
<td> </td>
<td> </td>
<td> </td>
<td> </td>
<td> </td>
<td bgcolor="#4357CFF">1st March </td>
<td bgcolor="#CCCCCC">2nd </td>
</tr>
<tr valign="top">
<td>3rd Richard away </td>
<td>4th '''(Vincent)''' Richard away </td>
<td>5th Richard away Vincent away </td>
<td>6th Richard away </td>
<td>7th Richard away </td>
<td bgcolor="#CCCCCC">8th </td>
<td bgcolor="#CCCCCC">9th </td>
</tr>
<tr valign="top">
<td>10th Richard away </td>
<td>11th '''(Becky)''' Richard away </td>
<td>12th Richard away </td>
<td>13th Richard away </td>
<td>14th Richard away </td>
<td bgcolor="#CCCCCC">15th </td>
<td bgcolor="#CCCCCC">16th </td>
</tr>
<tr valign="top">
<td>17th </td>
<td>18th '''(Giacomo)''' Richard postdoc workshop</td>
<td>19th </td>
<td>20th </td>
<td>21st Claire away</td>
<td bgcolor="#CCCCCC">22nd </td>
<td bgcolor="#CCCCCC">23rd </td>
</tr>
<tr valign="top">
<td>24th </td>
<td>25th '''(Patricia)'''</td>
<td>26th </td>
<td>27th </td>
<td bgcolor="#FFA500">28th '''End of term'''</td>
<td bgcolor="#CCCCCC">29th </td>
<td bgcolor="#CCCCCC">30th </td>
</tr>
<tr valign="top">
<td>31st Becky away rowing </td>
<td bgcolor="#4357CFF">1st April '''(Precious)''' DL_Poly workshop - Claire, Richard</td>
<td>2nd DL_Poly workshop - Claire, Richard Becky away rowing </td>
<td>3rd Becky away rowing </td>
<td>4th Becky away rowing </td>
<td bgcolor="#CCCCCC">5th Becky away rowing </td>
<td bgcolor="#CCCCCC">6th Becky away rowing </td>
</tr>
<tr valign="top">
<td>7th Becky away rowing </td>
<td >8th '''(Matthew)''' Becky away rowing </td>
<td>9th Matthew Away Becky away rowing </td>
<td>10th Matthew Away </td>
<td>11th Matthew Away </td>
<td bgcolor="#CCCCCC">12th </td>
<td bgcolor="#CCCCCC">13th </td>
</tr>
<tr valign="top">
<td>14th Bryan Away </td>
<td >15th Bryan Away '''(Group activity)'''</td>
<td>16th Tricia away Giacomo away </td>
<td bgcolor="#339933">17th '''College Closed'''</td>
<td bgcolor="#339933">18th '''College Closed'''</td>
<td bgcolor="#CCCCCC">19th '''College Closed'''</td>
<td bgcolor="#CCCCCC">20th '''College Closed'''</td>
</tr>
<tr valign="top">
<td bgcolor="#339933">21st '''College Closed'''</td>
<td bgcolor="#339933" >22nd '''College Closed'''</td>
<td>23rd Tricia away Richard away Precious away Giacomo away Gabriel away </td>
<td>24th Richard away Giacomo away Gabriel away Precious away </td>
<td>25th Richard away Giacomo away Gabriel away </td>
<td bgcolor="#FFA500">26th '''Start of term''' Giacomo away </td>
<td bgcolor="#CCCCCC">27th Giacomo away </td>
</tr>
<tr valign="top">
<td>28th Giacomo away </td>
<td >29th </td>
<td>30th </td>
<td bgcolor="#4357CFF">1st May </td>
<td>2nd </td>
<td bgcolor="#CCCCCC">3rd </td>
<td bgcolor="#CCCCCC">4th </td>
</tr>
<tr valign="top">
<td bgcolor="#339933">5th '''College Closed''' '''Bank holiday'''</td>
<td >6th '''(Tricia-DFT functionals)'''</td>
<td>7th </td>
<td>8th </td>
<td>9th </td>
<td bgcolor="#CCCCCC">10th </td>
<td bgcolor="#CCCCCC">11th </td>
</tr>
<tr valign="top">
<td >12th </td>
<td >13th </td>
<td>14th </td>
<td>15th </td>
<td>16th </td>
<td bgcolor="#CCCCCC">17th </td>
<td bgcolor="#CCCCCC">18th </td>
</tr>
<tr valign="top">
<td >19th </td>
<td >20th </td>
<td>21st </td>
<td>22nd </td>
<td>23rd </td>
<td bgcolor="#CCCCCC">24th </td>
<td bgcolor="#CCCCCC">25th </td>
</tr>
<tr valign="top">
<td bgcolor="#339933">26th '''College closed''' '''Bank holiday'''</td>
<td >27th </td>
<td>28th </td>
<td>29th </td>
<td>30th </td>
<td bgcolor="#CCCCCC">31st </td>
<td bgcolor="#4357CFF">1st June </td>
</tr>
<tr valign="top">
<td>2nd </td>
<td>3rd </td>
<td>4th CECAM workshop</td>
<td>5th CECAM workshop Claire away</td>
<td>6th CECAM workshop Claire away</td>
<td bgcolor="#CCCCCC">7th </td>
<td bgcolor="#CCCCCC">8th </td>
</tr>
<tr valign="top">
<td>9th </td>
<td>10th </td>
<td>11th </td>
<td>12th </td>
<td>13th </td>
<td bgcolor="#CCCCCC">14th </td>
<td bgcolor="#CCCCCC">15th </td>
</tr>
<tr valign="top">
<td>16th </td>
<td>17th </td>
<td>18th </td>
<td>19th </td>
<td>20th </td>
<td bgcolor="#CCCCCC">21st </td>
<td bgcolor="#CCCCCC">22nd </td>
</tr>
<tr valign="top">
<td>23rd </td>
<td>24th </td>
<td>25th </td>
<td>26th </td>
<td bgcolor="#FFA500">27th '''End of term'''</td>
<td bgcolor="#CCCCCC">28th </td>
<td bgcolor="#CCCCCC">29th </td>
</tr>
<tr valign="top">
<td>30th </td>
<td bgcolor="#4357CFF" >1st July {{fontcolor|#FFD700|'''PhD Symposium (Chem.)'''}}</td>
<td>2nd </td>
<td>3rd </td>
<td>4th </td>
<td bgcolor="#CCCCCC">5th </td>
<td bgcolor="#CCCCCC">6th EUCHEM</td>
</tr>
<tr valign="top">
<td>7th EUCHEM</td>
<td>8th EUCHEM</td>
<td>9th EUCHEM</td>
<td>10th EUCHEM</td>
<td>11th EUCHEM</td>
<td bgcolor="#CCCCCC">12th </td>
<td bgcolor="#CCCCCC">13th </td>
</tr>
<tr valign="top">
<td>14th Richard away</td>
<td>15th Richard away</td>
<td>16th Richard away</td>
<td>17th Richard away</td>
<td>18th Richard away</td>
<td bgcolor="#CCCCCC">19th </td>
<td bgcolor="#CCCCCC">20th </td>
</tr>
<tr valign="top">
<td>21st </td>
<td>22nd </td>
<td>23rd Gaussian workshop - Claire</td>
<td>24th Gaussian workshop - Claire</td>
<td>25th </td>
<td bgcolor="#CCCCCC">26th </td>
<td bgcolor="#CCCCCC">27th </td>
</tr>

<tr valign="top">
<td>28th </td>
<td>29th </td>
<td>30th </td>
<td>31st </td>
<td bgcolor="#4357CFF">1st August </td>
<td bgcolor="#CCCCCC">2nd </td>
<td bgcolor="#CCCCCC">3rd </td>
</tr>
</table>

Mod:Hunt Research Group/calendar

2014-02-13T17:00:36Z

Vhc08:

== Calendar ==

*Tricia (Not Done)
*Abdihakim Hassan (Not Done)
*Bryan Ward (Not Done)
*Claire Ashworth (Not Done)
*Matthew Clough (Not Done)
*Precious Ugbomah (Not Done)
*Richard Matthews (Done)
*Vincent Chen (Not Done)
*Gabriel Lau (Not Done)
*Rebecca Rowe (Not Done)
*Patricia Ho (Not Done)
*Giacomo Damilano (Not Done)

<table border="1" cellpadding="5" width="1190">
<tr bgcolor="#66CCFF">
<th width="170px">Mon</th>
<th width="170px">Tues</th>
<th width="170px">Wed</th>
<th width="170px">Thur</th>
<th width="170px">Fri</th>
<th width="170px" bgcolor="#CCCCCC">Sat</th>
<th width="170px" bgcolor="#CCCCCC">Sun</th>
<tr valign="top">
<td > </td>
<td > </td>
<td bgcolor="#4357CFF">1st January '''College closed'''</td>
<td>2nd Richard away Claire away Tricia away Giacomo Away Patricia away Precious away</td>
<td>3rd Richard away Gabriel & Vincent - Science Communication Course Bryan Away Tricia away Giacomo Away Patricia away Precious away</td>
<td bgcolor="#CCCCCC">4th Gabriel & Vincent - Science Communication Course Bryan Away Tricia away Giacomo Away Patricia away Precious away</td>
<td bgcolor="#CCCCCC">5th Gabriel & Vincent - Science Communication Course Bryan Away Tricia away Giacomo Away Patricia away Precious away</td>
</tr>
<tr valign="top">
<td>6th Bryan Away Precious away Patricia away</td>
<td>7th Bryan Away Precious away Patricia away</td>
<td>8th Bryan Away Patricia away Precious away</td>
<td>9th Bryan Away Patricia away</td>
<td>10th Bryan Away Patricia away Claire-MSDG</td>
<td bgcolor="#FFA500">11th '''Start of term'''</td>
<td bgcolor="#CCCCCC">12th </td>
</tr>
<tr valign="top">
<td>13th Vincent Away</td>
<td>14th Vincent Away</td>
<td>15th Vincent Away</td>
<td>16th Vincent Away</td>
<td>17th Vincent Away</td>
<td bgcolor="#CCCCCC">18th </td>
<td bgcolor="#CCCCCC">19th </td>
</tr>
<tr valign="top">
<td>20th Vincent Away</td>
<td>21st '''(Bryan)''' Vincent Away</td>
<td>22nd Vincent Away</td>
<td>23rd Vincent Away</td>
<td>24th Vincent Away Claire away</td>
<td bgcolor="#CCCCCC">25th Claire away</td>
<td bgcolor="#CCCCCC">26th Claire away</td>
</tr>
<tr valign="top">
<td>27th Claire away Vincent Away</td>
<td>28th '''(Gabriel)''' Claire away Vincent Away</td>
<td>29th Claire away Vincent Away</td>
<td>30th Claire away Vincent Away</td>
<td>31st Claire away Vincent Away</td>
<td bgcolor="#4357CFF">1st February Claire away</td>
<td bgcolor="#CCCCCC">2nd Claire away</td>
</tr>
<tr valign="top">
<td>3rd Claire away</td>
<td>4th '''(Hakim)''' Claire away</td>
<td>5th Claire away</td>
<td>6th Claire away</td>
<td>7th Claire away</td>
<td bgcolor="#CCCCCC">8th </td>
<td bgcolor="#CCCCCC">9th </td>
</tr>
<tr valign="top">
<td>10th </td>
<td>11th '''(Matthew)'''</td>
<td>12th </td>
<td>13th </td>
<td>14th </td>
<td bgcolor="#CCCCCC">15th </td>
<td bgcolor="#CCCCCC">16th </td>
</tr>
<tr valign="top">
<td>17th </td>
<td>18th '''(Richard)'''</td>
<td>19th </td>
<td>20th </td>
<td>21st </td>
<td bgcolor="#CCCCCC">22nd </td>
<td bgcolor="#CCCCCC">23rd </td>
</tr>
<tr valign="top">
<td>24th </td>
<td>25th '''(Claire)'''</td>
<td>26th </td>
<td>27th </td>
<td>28th </td>
<td bgcolor="#4357CFF">1st March </td>
<td bgcolor="#CCCCCC">2nd </td>
</tr>
<tr valign="top">
<td>3rd Richard away </td>
<td>4th '''(Vincent)''' Richard away </td>
<td>5th Richard away Vincent away </td>
<td>6th Richard away </td>
<td>7th Richard away </td>
<td bgcolor="#CCCCCC">8th </td>
<td bgcolor="#CCCCCC">9th </td>
</tr>
<tr valign="top">
<td>10th Richard away </td>
<td>11th '''(Becky)''' Richard away </td>
<td>12th Richard away </td>
<td>13th Richard away </td>
<td>14th Richard away </td>
<td bgcolor="#CCCCCC">15th </td>
<td bgcolor="#CCCCCC">16th </td>
</tr>
<tr valign="top">
<td>17th </td>
<td>18th '''(Giacomo)'''</td>
<td>19th </td>
<td>20th </td>
<td>21st </td>
<td bgcolor="#CCCCCC">22nd </td>
<td bgcolor="#CCCCCC">23rd </td>
</tr>
<tr valign="top">
<td>24th </td>
<td>25th '''(Patricia)'''</td>
<td>26th </td>
<td>27th </td>
<td bgcolor="#FFA500">28th '''End of term'''</td>
<td bgcolor="#CCCCCC">29th </td>
<td bgcolor="#CCCCCC">30th </td>
</tr>
<tr valign="top">
<td>31st </td>
<td bgcolor="#4357CFF">1st April '''(Precious)'''</td>
<td>2nd </td>
<td>3rd </td>
<td>4th </td>
<td bgcolor="#CCCCCC">5th </td>
<td bgcolor="#CCCCCC">6th </td>
</tr>
<tr valign="top">
<td>7th </td>
<td >8th '''(Tricia & DFT functionals)'''</td>
<td>9th </td>
<td>10th </td>
<td>11th </td>
<td bgcolor="#CCCCCC">12th </td>
<td bgcolor="#CCCCCC">13th </td>
</tr>
<tr valign="top">
<td>14th </td>
<td >15th </td>
<td>16th </td>
<td bgcolor="#339933">17th '''College Closed'''</td>
<td bgcolor="#339933">18th '''College Closed'''</td>
<td bgcolor="#CCCCCC">19th '''College Closed'''</td>
<td bgcolor="#CCCCCC">20th '''College Closed'''</td>
</tr>
<tr valign="top">
<td bgcolor="#339933">21st '''College Closed'''</td>
<td bgcolor="#339933" >22nd '''College Closed'''</td>
<td>23rd </td>
<td>24th </td>
<td>25th </td>
<td bgcolor="#FFA500">26th '''Start of term'''</td>
<td bgcolor="#CCCCCC">27th </td>
</tr>
<tr valign="top">
<td>28th </td>
<td >29th </td>
<td>30th </td>
<td bgcolor="#4357CFF">1st May </td>
<td>2nd </td>
<td bgcolor="#CCCCCC">3rd </td>
<td bgcolor="#CCCCCC">4th </td>
</tr>
<td bgcolor="#339933">5th '''College Closed''' '''Bank holiday'''</td>
<td >6th </td>
<td>7th </td>
<td>8th </td>
<td>9th </td>
<td bgcolor="#CCCCCC">10th </td>
<td bgcolor="#CCCCCC">11th </td>

</table>

Mod:Hunt Research Group/calendar

2014-01-27T23:35:24Z

Vhc08: /* Calendar */

== Calendar ==

*Tricia (Not Done)
*Abdihakim Hassan (Not Done)
*Bryan Ward (Not Done)
*Claire Ashworth (Not Done)
*Matthew Clough (Not Done)
*Precious Ugbomah (Not Done)
*Richard Matthews (Done)
*Vincent Chen (Not Done)
*Gabriel Lau (Not Done)
*Rebecca Rowe (Not Done)
*Patricia Ho (Not Done)
*Giacomo Damilano (Not Done)

<table border="1" cellpadding="5" width="1190">
<tr bgcolor="#66CCFF">
<th width="170px">Mon</th>
<th width="170px">Tues</th>
<th width="170px">Wed</th>
<th width="170px">Thur</th>
<th width="170px">Fri</th>
<th width="170px" bgcolor="#CCCCCC">Sat</th>
<th width="170px" bgcolor="#CCCCCC">Sun</th>
<tr valign="top">
<td > </td>
<td > </td>
<td bgcolor="#4357CFF">1st January '''College closed'''</td>
<td>2nd Richard away Claire away Tricia away Giacomo Away Patricia away Precious away</td>
<td>3rd Richard away Gabriel & Vincent - Science Communication Course Bryan Away Tricia away Giacomo Away Patricia away Precious away</td>
<td bgcolor="#CCCCCC">4th Gabriel & Vincent - Science Communication Course Bryan Away Tricia away Giacomo Away Patricia away Precious away</td>
<td bgcolor="#CCCCCC">5th Gabriel & Vincent - Science Communication Course Bryan Away Tricia away Giacomo Away Patricia away Precious away</td>
</tr>
<tr valign="top">
<td>6th Bryan Away Precious away Patricia away</td>
<td>7th Bryan Away Precious away Patricia away</td>
<td>8th Bryan Away Patricia away Precious away</td>
<td>9th Bryan Away Patricia away</td>
<td>10th Bryan Away Patricia away Claire-MSDG</td>
<td bgcolor="#FFA500">11th '''Start of term'''</td>
<td bgcolor="#CCCCCC">12th </td>
</tr>
<tr valign="top">
<td>13th Vincent Away</td>
<td>14th Vincent Away</td>
<td>15th Vincent Away</td>
<td>16th Vincent Away</td>
<td>17th Vincent Away</td>
<td bgcolor="#CCCCCC">18th </td>
<td bgcolor="#CCCCCC">19th </td>
</tr>
<tr valign="top">
<td>20th Vincent Away</td>
<td>21st '''(Bryan)''' Vincent Away</td>
<td>22nd Vincent Away</td>
<td>23rd Vincent Away</td>
<td>24th Vincent Away Claire away</td>
<td bgcolor="#CCCCCC">25th Claire away</td>
<td bgcolor="#CCCCCC">26th Claire away</td>
</tr>
<tr valign="top">
<td>27th Claire away Vincent Away</td>
<td>28th '''(Gabriel)''' Claire away Vincent Away</td>
<td>29th Claire away Vincent Away</td>
<td>30th Claire away Vincent Away</td>
<td>31st Claire away Vincent Away</td>
<td bgcolor="#4357CFF">1st February Claire away</td>
<td bgcolor="#CCCCCC">2nd Claire away</td>
</tr>
<tr valign="top">
<td>3rd Claire away</td>
<td>4th '''(Hakim)''' Claire away</td>
<td>5th Claire away</td>
<td>6th Claire away</td>
<td>7th Claire away</td>
<td bgcolor="#CCCCCC">8th </td>
<td bgcolor="#CCCCCC">9th </td>
</tr>
<tr valign="top">
<td>10th </td>
<td>11th '''(Matthew)'''</td>
<td>12th </td>
<td>13th </td>
<td>14th </td>
<td bgcolor="#CCCCCC">15th </td>
<td bgcolor="#CCCCCC">16th </td>
</tr>
<tr valign="top">
<td>17th </td>
<td>18th '''(Richard)'''</td>
<td>19th </td>
<td>20th </td>
<td>21st </td>
<td bgcolor="#CCCCCC">22nd </td>
<td bgcolor="#CCCCCC">23rd </td>
</tr>
<tr valign="top">
<td>24th </td>
<td>25th '''(Claire)'''</td>
<td>26th </td>
<td>27th </td>
<td>28th </td>
<td bgcolor="#4357CFF">1st March </td>
<td bgcolor="#CCCCCC">2nd </td>
</tr>
<tr valign="top">
<td>3rd Richard away </td>
<td>4th '''(Vincent)''' Richard away </td>
<td>5th Richard away </td>
<td>6th Richard away </td>
<td>7th Richard away </td>
<td bgcolor="#CCCCCC">8th </td>
<td bgcolor="#CCCCCC">9th </td>
</tr>
<tr valign="top">
<td>10th Richard away </td>
<td>11th '''(Becky)''' Richard away </td>
<td>12th Richard away </td>
<td>13th Richard away </td>
<td>14th Richard away </td>
<td bgcolor="#CCCCCC">15th </td>
<td bgcolor="#CCCCCC">16th </td>
</tr>
<tr valign="top">
<td>17th </td>
<td>18th '''(Giacomo)'''</td>
<td>19th </td>
<td>20th </td>
<td>21st </td>
<td bgcolor="#CCCCCC">22nd </td>
<td bgcolor="#CCCCCC">23rd </td>
</tr>
<tr valign="top">
<td>24th </td>
<td>25th '''(Patricia)'''</td>
<td>26th </td>
<td>27th </td>
<td bgcolor="#FFA500">28th '''End of term'''</td>
<td bgcolor="#CCCCCC">29th </td>
<td bgcolor="#CCCCCC">30th </td>
</tr>
<tr valign="top">
<td>31st </td>
<td bgcolor="#4357CFF">1st April '''(Precious)'''</td>
<td>2nd </td>
<td>3rd </td>
<td>4th </td>
<td bgcolor="#CCCCCC">5th </td>
<td bgcolor="#CCCCCC">6th </td>
</tr>
<tr valign="top">
<td>7th </td>
<td >8th '''(Tricia & DFT functionals)'''</td>
<td>9th </td>
<td>10th </td>
<td>11th </td>
<td bgcolor="#CCCCCC">12th </td>
<td bgcolor="#CCCCCC">13th </td>
</tr>
<tr valign="top">
<td>14th </td>
<td >15th </td>
<td>16th </td>
<td bgcolor="#339933">17th '''College Closed'''</td>
<td bgcolor="#339933">18th '''College Closed'''</td>
<td bgcolor="#CCCCCC">19th '''College Closed'''</td>
<td bgcolor="#CCCCCC">20th '''College Closed'''</td>
</tr>
<tr valign="top">
<td bgcolor="#339933">21st '''College Closed'''</td>
<td bgcolor="#339933" >22nd '''College Closed'''</td>
<td>23rd </td>
<td>24th </td>
<td>25th </td>
<td bgcolor="#FFA500">26th '''Start of term'''</td>
<td bgcolor="#CCCCCC">27th </td>
</tr>
<tr valign="top">
<td>28th </td>
<td >29th </td>
<td>30th </td>
<td bgcolor="#4357CFF">1st May </td>
<td>2nd </td>
<td bgcolor="#CCCCCC">3rd </td>
<td bgcolor="#CCCCCC">4th </td>
</tr>
<td bgcolor="#339933">5th '''College Closed''' '''Bank holiday'''</td>
<td >6th </td>
<td>7th </td>
<td>8th </td>
<td>9th </td>
<td bgcolor="#CCCCCC">10th </td>
<td bgcolor="#CCCCCC">11th </td>

</table>

Mod:Hunt Research Group/calendar

2013-11-26T11:57:20Z

Vhc08:

== Calendar ==

*Tricia (Done)
*Abdihakim Hassan (Not Done)
*Bryan Ward (Done)
*Claire Ashworth (Done)
*Matthew Clough (Not Done)
*Precious Ugbomah (Not Done)
*Richard Matthews (Done)
*Vincent Chen (Done)
*Gabriel Lau (Done)
*Rebecca Rowe (Not Done)
*Patricia Ho (Done)
*Giacomo Damilano (Done)

<table border="1" cellpadding="5" width="1190">
<tr bgcolor="#66CCFF">
<th width="170px">Mon</th>
<th width="170px">Tues</th>
<th width="170px">Wed</th>
<th width="170px">Thur</th>
<th width="170px">Fri</th>
<th width="170px" bgcolor="#CCCCCC">Sat</th>
<th width="170px" bgcolor="#CCCCCC">Sun</th>

<tr valign="top">
<td>28th </td>
<td>29th '''(Matthew)'''</td>
<td>30th </td>
<td>31st </td>
<td bgcolor="#4357CFF">1st November </td>
<td bgcolor="#CCCCCC">2nd </td>
<td bgcolor="#CCCCCC">3rd </td>
</tr>
<tr valign="top">
<td>4th </td>
<td>5th '''(Vincent)'''</td>
<td>6th </td>
<td>7th </td>
<td>8th</td>
<td bgcolor="#CCCCCC">9th </td>
<td bgcolor="#CCCCCC">10th </td>
</tr>
<tr valign="top">
<td>11th </td>
<td>12th '''(Gabriel)'''</td>
<td>13th </td>
<td>14th </td>
<td>15th</td>
<td bgcolor="#CCCCCC">16th </td>
<td bgcolor="#CCCCCC">17th </td>
</tr>
<tr valign="top">
<td>18th </td>
<td>19th '''(Hakim)'''</td>
<td>20th </td>
<td>21st </td>
<td>22nd</td>
<td bgcolor="#CCCCCC">23rd </td>
<td bgcolor="#CCCCCC">24th </td>
</tr>
<tr valign="top">
<td>25th </td>
<td>26th '''(Group Outing)'''</td>
<td>27th </td>
<td>28th </td>
<td>29th</td>
<td bgcolor="#CCCCCC">30th </td>
<td bgcolor="#4357CFF">1st December </td>
</tr>
<tr valign="top">
<td>2nd </td>
<td>3rd '''(Richard)''' Bryan Away Vincent Away</td>
<td>4th Bryan Away</td>
<td>5th Bryan Away</td>
<td>6th Bryan Away</td>
<td bgcolor="#CCCCCC">7th Bryan Away</td>
<td bgcolor="#CCCCCC">8th Bryan Away</td>
</tr>
<tr valign="top">
<td>9th Bryan Away</td>
<td>10th '''(Becky)''' Bryan Away</td>
<td>11th </td>
<td>12th </td>
<td bgcolor="#FFA500">13th '''End of term''' Giacomo Away Patricia away</td>
<td bgcolor="#CCCCCC">14th Giacomo Away Patricia away</td>
<td bgcolor="#CCCCCC">15th Giacomo Away Patricia away</td>
</tr>
<tr valign="top">
<td>16th Giacomo Away Patricia away</td>
<td>17th '''(CV Workshop)''' Giacomo Away Patricia away</td>
<td>18th Giacomo Away Patricia away</td>
<td>19th Giacomo Away Patricia away</td>
<td>20th Giacomo Away Patricia away</td>
<td bgcolor="#CCCCCC">21st Giacomo Away Patricia away</td>
<td bgcolor="#CCCCCC">22nd Giacomo Away Patricia away</td>
</tr>
<tr valign="top">
<td bgcolor="#228B22">23rd '''College closed'''</td>
<td bgcolor="#228B22">24th '''College closed'''</td>
<td bgcolor="#228B22">25th '''College closed'''</td>
<td bgcolor="#228B22">26th '''College closed'''</td>
<td bgcolor="#228B22">27th '''College closed'''</td>
<td bgcolor="#228B22">28th '''College closed'''</td>
<td bgcolor="#228B22">29th '''College closed'''</td>
</tr>
<tr valign="top">
<td bgcolor="#228B22">30th '''College closed'''</td>
<td bgcolor="#228B22">31st '''College closed'''</td>
<td bgcolor="#4357CFF">1st January '''College closed'''</td>
<td>2nd Richard away Claire away Tricia away Giacomo Away Patricia away</td>
<td>3rd Richard away Gabriel & Vincent - Science Communication Course Bryan Away Tricia away Giacomo Away Patricia away</td>
<td bgcolor="#CCCCCC">4th Gabriel & Vincent - Science Communication Course Bryan Away Tricia away Giacomo Away Patricia away</td>
<td bgcolor="#CCCCCC">5th Gabriel & Vincent - Science Communication Course Bryan Away Tricia away Giacomo Away Patricia away</td>
</tr>
<tr valign="top">
<td>6th Bryan Away</td>
<td>7th Bryan Away</td>
<td>8th Bryan Away</td>
<td>9th Bryan Away</td>
<td>10th Bryan Away</td>
<td bgcolor="#FFA500">11th '''Start of term'''</td>
<td bgcolor="#CCCCCC">12th </td>
</tr>
<tr valign="top">
<td>13th Vincent Away</td>
<td>14th Vincent Away</td>
<td>15th Vincent Away</td>
<td>16th Vincent Away</td>
<td>17th Vincent Away</td>
<td bgcolor="#CCCCCC">18th </td>
<td bgcolor="#CCCCCC">19th </td>
</tr>
<tr valign="top">
<td>20th Vincent Away</td>
<td>21st Vincent Away</td>
<td>22nd Vincent Away</td>
<td>23rd Vincent Away</td>
<td>24th Vincent Away</td>
<td bgcolor="#CCCCCC">25th </td>
<td bgcolor="#CCCCCC">26th </td>
</tr>
</table>

Mod:Hunt Research Group/calendar

2013-11-26T11:55:18Z

Vhc08:

== Calendar ==

*Tricia (Done)
*Abdihakim Hassan (Not Done)
*Bryan Ward (Done)
*Claire Ashworth (Done)
*Matthew Clough (Not Done)
*Precious Ugbomah (Not Done)
*Richard Matthews (Done)
*Vincent Chen (Not Done)
*Gabriel Lau (Done)
*Rebecca Rowe (Not Done)
*Patricia Ho (Done)
*Giacomo Damilano (Done)

<table border="1" cellpadding="5" width="1190">
<tr bgcolor="#66CCFF">
<th width="170px">Mon</th>
<th width="170px">Tues</th>
<th width="170px">Wed</th>
<th width="170px">Thur</th>
<th width="170px">Fri</th>
<th width="170px" bgcolor="#CCCCCC">Sat</th>
<th width="170px" bgcolor="#CCCCCC">Sun</th>

<tr valign="top">
<td>28th </td>
<td>29th '''(Matthew)'''</td>
<td>30th </td>
<td>31st </td>
<td bgcolor="#4357CFF">1st November </td>
<td bgcolor="#CCCCCC">2nd </td>
<td bgcolor="#CCCCCC">3rd </td>
</tr>
<tr valign="top">
<td>4th </td>
<td>5th '''(Vincent)'''</td>
<td>6th </td>
<td>7th </td>
<td>8th</td>
<td bgcolor="#CCCCCC">9th </td>
<td bgcolor="#CCCCCC">10th </td>
</tr>
<tr valign="top">
<td>11th </td>
<td>12th '''(Gabriel)'''</td>
<td>13th </td>
<td>14th </td>
<td>15th</td>
<td bgcolor="#CCCCCC">16th </td>
<td bgcolor="#CCCCCC">17th </td>
</tr>
<tr valign="top">
<td>18th </td>
<td>19th '''(Hakim)'''</td>
<td>20th </td>
<td>21st </td>
<td>22nd</td>
<td bgcolor="#CCCCCC">23rd </td>
<td bgcolor="#CCCCCC">24th </td>
</tr>
<tr valign="top">
<td>25th </td>
<td>26th '''(Group Outing)'''</td>
<td>27th </td>
<td>28th </td>
<td>29th</td>
<td bgcolor="#CCCCCC">30th </td>
<td bgcolor="#4357CFF">1st December </td>
</tr>
<tr valign="top">
<td>2nd </td>
<td>3rd '''(Richard)''' Bryan Away Vincent Away</td>
<td>4th Bryan Away</td>
<td>5th Bryan Away</td>
<td>6th Bryan Away</td>
<td bgcolor="#CCCCCC">7th Bryan Away</td>
<td bgcolor="#CCCCCC">8th Bryan Away</td>
</tr>
<tr valign="top">
<td>9th Bryan Away</td>
<td>10th '''(Becky)''' Bryan Away</td>
<td>11th </td>
<td>12th </td>
<td bgcolor="#FFA500">13th '''End of term''' Giacomo Away Patricia away</td>
<td bgcolor="#CCCCCC">14th Giacomo Away Patricia away</td>
<td bgcolor="#CCCCCC">15th Giacomo Away Patricia away</td>
</tr>
<tr valign="top">
<td>16th Giacomo Away Patricia away</td>
<td>17th '''(CV Workshop)''' Giacomo Away Patricia away</td>
<td>18th Giacomo Away Patricia away</td>
<td>19th Giacomo Away Patricia away</td>
<td>20th Giacomo Away Patricia away</td>
<td bgcolor="#CCCCCC">21st Giacomo Away Patricia away</td>
<td bgcolor="#CCCCCC">22nd Giacomo Away Patricia away</td>
</tr>
<tr valign="top">
<td bgcolor="#228B22">23rd '''College closed'''</td>
<td bgcolor="#228B22">24th '''College closed'''</td>
<td bgcolor="#228B22">25th '''College closed'''</td>
<td bgcolor="#228B22">26th '''College closed'''</td>
<td bgcolor="#228B22">27th '''College closed'''</td>
<td bgcolor="#228B22">28th '''College closed'''</td>
<td bgcolor="#228B22">29th '''College closed'''</td>
</tr>
<tr valign="top">
<td bgcolor="#228B22">30th '''College closed'''</td>
<td bgcolor="#228B22">31st '''College closed'''</td>
<td bgcolor="#4357CFF">1st January '''College closed'''</td>
<td>2nd Richard away Claire away Tricia away Giacomo Away Patricia away</td>
<td>3rd Richard away Gabriel & Vincent - Science Communication Course Bryan Away Tricia away Giacomo Away Patricia away</td>
<td bgcolor="#CCCCCC">4th Gabriel & Vincent - Science Communication Course Bryan Away Tricia away Giacomo Away Patricia away</td>
<td bgcolor="#CCCCCC">5th Gabriel & Vincent - Science Communication Course Bryan Away Tricia away Giacomo Away Patricia away</td>
</tr>
<tr valign="top">
<td>6th Bryan Away</td>
<td>7th Bryan Away</td>
<td>8th Bryan Away</td>
<td>9th Bryan Away</td>
<td>10th Bryan Away</td>
<td bgcolor="#FFA500">11th '''Start of term'''</td>
<td bgcolor="#CCCCCC">12th </td>
</tr>
<tr valign="top">
<td>13th Vincent Away</td>
<td>14th Vincent Away</td>
<td>15th Vincent Away</td>
<td>16th Vincent Away</td>
<td>17th Vincent Away</td>
<td bgcolor="#CCCCCC">18th </td>
<td bgcolor="#CCCCCC">19th </td>
</tr>
<tr valign="top">
<td>20th Vincent Away</td>
<td>21st Vincent Away</td>
<td>22nd Vincent Away</td>
<td>23rd Vincent Away</td>
<td>24th Vincent Away</td>
<td bgcolor="#CCCCCC">25th </td>
<td bgcolor="#CCCCCC">26th </td>
</tr>
</table>

Mod:Hunt Research Group/calendar

2013-10-02T11:40:48Z

Vhc08:

== Calendar ==

*Tricia (Done)
*Abdihakim Hassan (Not Done)
*Bryan Ward (Not Done)
*Claire Ashworth (Not Done)
*Matthew Clough (Done)
*Precious Ugbomah (Done)
*Richard Matthews (Done)
*Vincent Chen (Done)
*Gabriel Lau (Done)
*Sarah Smith (Not Done)

{| class="wikitable" border="1" style="text-align:center"
|+ Theory Group Meetings: 2-3.30pm every other Thursday
!Meeting !! Topic || Name || Date
|-
| <s>1</s> || <s>Differentiation and Integration</s> || Matthew || <s>20th June</s>
|-
| <s>2</s> || <s>Differential Equations</s> || Claire || <s>27th</s> <s>June</s>
|-
| 3|| <s>Matrix Mechanics</s> ||Gabriel|| <s>1st August</s>
|-
| 4 || Linear Algebra || Richard || Postponed
|-
| 5 || Chem. I - topic TBD ||Bryan || Postponed
|-
| 6 ||Perturbation Theory|| Vincent|| Postponed
|}

<table border="1" cellpadding="5" width="1190">
<tr bgcolor="#66CCFF">
<th width="170px">Mon</th>
<th width="170px">Tues</th>
<th width="170px">Wed</th>
<th width="170px">Thur</th>
<th width="170px">Fri</th>
<th width="170px" bgcolor="#CCCCCC">Sat</th>
<th width="170px" bgcolor="#CCCCCC">Sun</th>
<tr valign="top">
<td>16th </td>
<td>17th Bryan/Claire - Gaussian Workshop</td>
<td>18th Bryan/Claire - Gaussian Workshop</td>
<td>19th </td>
<td>20th '''(Sarah)'''</td>
<td bgcolor="#CCCCCC">21st </td>
<td bgcolor="#CCCCCC">22nd </td>
</tr>
<tr valign="top">
<td>23rd </td>
<td>24th </td>
<td>25th </td>
<td>26th </td>
<td>27th Claire away</td>
<td bgcolor="#FFA500">28th '''Start of Term'''</td>
<td bgcolor="#CCCCCC">29th </td>
</tr>
<tr valign="top">
<td>30th Claire away</td>
<td bgcolor="#4357CFF">1st October '''(Paper)''' Claire away</td>
<td>2nd Claire away</td>
<td>3rd Claire away</td>
<td>4th Claire away </td>
<td bgcolor="#CCCCCC">5th </td>
<td bgcolor="#CCCCCC">6th </td>
</tr>
<tr valign="top">
<td>7th </td>
<td>8th '''(Precious)'''</td>
<td>9th </td>
<td>10th '''Theory Meeting'''</td>
<td>11th </td>
<td bgcolor="#CCCCCC">12th </td>
<td bgcolor="#CCCCCC">13th </td>
</tr>
<tr valign="top">
<td>14th </td>
<td>15th '''(Claire)'''</td>
<td>16th </td>
<td>17th </td>
<td>18th </td>
<td bgcolor="#CCCCCC">19th </td>
<td bgcolor="#CCCCCC">20th </td>
</tr>
<tr valign="top">
<td>21st </td>
<td>22nd '''(Bryan)'''</td>
<td>23rd </td>
<td>24th </td>
<td>25th </td>
<td bgcolor="#CCCCCC">26th </td>
<td bgcolor="#CCCCCC">27th </td>
</tr>
<tr valign="top">
<td>28th </td>
<td>29th '''(Matthew)'''</td>
<td>30th </td>
<td>31st </td>
<td bgcolor="#4357CFF">1st November </td>
<td bgcolor="#CCCCCC">2nd </td>
<td bgcolor="#CCCCCC">3rd </td>
</tr>
<tr valign="top">
<td>4th </td>
<td>5th '''(Vincent)'''</td>
<td>6th </td>
<td>7th </td>
<td>8th</td>
<td bgcolor="#CCCCCC">9th </td>
<td bgcolor="#CCCCCC">10th </td>
</tr>
<tr valign="top">
<td>11th </td>
<td>12th '''(Gabriel)'''</td>
<td>13th </td>
<td>14th </td>
<td>15th</td>
<td bgcolor="#CCCCCC">16th </td>
<td bgcolor="#CCCCCC">17th </td>
</tr>
<tr valign="top">
<td>18th </td>
<td>19th </td>
<td>20th </td>
<td>21st </td>
<td>22nd</td>
<td bgcolor="#CCCCCC">23rd </td>
<td bgcolor="#CCCCCC">24th </td>
</tr>
<tr valign="top">
<td>25th </td>
<td>26th </td>
<td>27th </td>
<td>28th </td>
<td>29th</td>
<td bgcolor="#CCCCCC">30th </td>
<td bgcolor="#4357CFF">1st December </td>
</tr>
<tr valign="top">
<td>2nd </td>
<td>3rd </td>
<td>4th </td>
<td>5th </td>
<td>6th</td>
<td bgcolor="#CCCCCC">7th </td>
<td bgcolor="#CCCCCC">8th </td>
</tr>
<tr valign="top">
<td>9th </td>
<td>10th </td>
<td>11th </td>
<td>12th </td>
<td bgcolor="#FFA500">13th '''End of term'''</td>
<td bgcolor="#CCCCCC">14th </td>
<td bgcolor="#CCCCCC">15th </td>
</tr>
<tr valign="top">
<td>16th </td>
<td>17th </td>
<td>18th </td>
<td>19th </td>
<td>20th </td>
<td bgcolor="#CCCCCC">21st </td>
<td bgcolor="#CCCCCC">22nd </td>
</tr>
<tr valign="top">
<td bgcolor="#228B22">23rd '''College closed'''</td>
<td bgcolor="#228B22">24th '''College closed'''</td>
<td bgcolor="#228B22">25th '''College closed'''</td>
<td bgcolor="#228B22">26th '''College closed'''</td>
<td bgcolor="#228B22">27th '''College closed'''</td>
<td bgcolor="#228B22">28th '''College closed'''</td>
<td bgcolor="#228B22">29th '''College closed'''</td>
</tr>
<tr valign="top">
<td bgcolor="#228B22">30th '''College closed'''</td>
<td bgcolor="#228B22">31st '''College closed'''</td>
<td bgcolor="#228B22">1st January '''College closed'''</td>
<td>2nd </td>
<td>3rd Gabriel & Vincent - Science Communication Course</td>
<td bgcolor="#CCCCCC">4th Gabriel & Vincent - Science Communication Course</td>
<td bgcolor="#CCCCCC">5th Gabriel & Vincent - Science Communication Course</td>
</tr>
</table>

Mod:Hunt Research Group/calendar

2013-10-02T11:40:34Z

Vhc08:

== Calendar ==

*Tricia (Done)
*Abdihakim Hassan (Not Done)
*Bryan Ward (Not Done)
*Claire Ashworth (Not Done)
*Matthew Clough (Done)
*Precious Ugbomah (Done)
*Richard Matthews (Done)
*Vincent Chen (Done)
*Gabriel Lau (Done)
*Sarah Smith (Not Done)

{| class="wikitable" border="1" style="text-align:center"
|+ Theory Group Meetings: 2-3.30pm every other Thursday
!Meeting !! Topic || Name || Date
|-
| <s>1</s> || <s>Differentiation and Integration</s> || Matthew || <s>20th June</s>
|-
| <s>2</s> || <s>Differential Equations</s> || Claire || <s>27th</s> <s>June</s>
|-
| 3|| <s>Matrix Mechanics</s> ||Gabriel|| <s>1st August</s>
|-
| 4 || Linear Algebra || Richard || Postponed
|-
| 5 || Chem. I - topic TBD ||Bryan || Postponed
|-
| 6 ||Perturbation Theory|| Vincent|| Postponed
|}

<table border="1" cellpadding="5" width="1190">
<tr bgcolor="#66CCFF">
<th width="170px">Mon</th>
<th width="170px">Tues</th>
<th width="170px">Wed</th>
<th width="170px">Thur</th>
<th width="170px">Fri</th>
<th width="170px" bgcolor="#CCCCCC">Sat</th>
<th width="170px" bgcolor="#CCCCCC">Sun</th>
<tr valign="top">
<td>16th </td>
<td>17th Bryan/Claire - Gaussian Workshop</td>
<td>18th Bryan/Claire - Gaussian Workshop</td>
<td>19th </td>
<td>20th '''(Sarah)'''</td>
<td bgcolor="#CCCCCC">21st </td>
<td bgcolor="#CCCCCC">22nd </td>
</tr>
<tr valign="top">
<td>23rd </td>
<td>24th </td>
<td>25th </td>
<td>26th </td>
<td>27th Claire away</td>
<td bgcolor="#FFA500">28th '''Start of Term'''</td>
<td bgcolor="#CCCCCC">29th </td>
</tr>
<tr valign="top">
<td>30th Claire away</td>
<td bgcolor="#4357CFF">1st October '''(Paper)''' Claire away</td>
<td>2nd Claire away</td>
<td>3rd Claire away</td>
<td>4th Claire away </td>
<td bgcolor="#CCCCCC">5th </td>
<td bgcolor="#CCCCCC">6th </td>
</tr>
<tr valign="top">
<td>7th </td>
<td>8th '''(Precious)'''</td>
<td>9th </td>
<td>10th '''Theory Meeting'''</td>
<td>11th </td>
<td bgcolor="#CCCCCC">12th </td>
<td bgcolor="#CCCCCC">13th </td>
</tr>
<tr valign="top">
<td>14th </td>
<td>15th '''(Claire)'''</td>
<td>16th </td>
<td>17th </td>
<td>18th </td>
<td bgcolor="#CCCCCC">19th </td>
<td bgcolor="#CCCCCC">20th </td>
</tr>
<tr valign="top">
<td>21st </td>
<td>22nd '''(Bryan)'''</td>
<td>23rd </td>
<td>24th </td>
<td>25th </td>
<td bgcolor="#CCCCCC">26th </td>
<td bgcolor="#CCCCCC">27th </td>
</tr>
<tr valign="top">
<td>28th </td>
<td>29th '''(Matthew)'''</td>
<td>30th </td>
<td>31st </td>
<td bgcolor="#4357CFF">1st November </td>
<td bgcolor="#CCCCCC">2nd </td>
<td bgcolor="#CCCCCC">3rd </td>
</tr>
<tr valign="top">
<td>4th </td>
<td>5th '''(Vincent)'''</td>
<td>6th </td>
<td>7th </td>
<td>8th</td>
<td bgcolor="#CCCCCC">9th </td>
<td bgcolor="#CCCCCC">10th </td>
</tr>
<tr valign="top">
<td>11th </td>
<td>12th '''(Gabriel)'''</td>
<td>13th </td>
<td>14th </td>
<td>15th</td>
<td bgcolor="#CCCCCC">16th </td>
<td bgcolor="#CCCCCC">17th </td>
</tr>
<tr valign="top">
<td>18th </td>
<td>19th </td>
<td>20th </td>
<td>21st </td>
<td>22nd</td>
<td bgcolor="#CCCCCC">23rd </td>
<td bgcolor="#CCCCCC">24th </td>
</tr>
<tr valign="top">
<td>25th </td>
<td>26th </td>
<td>27th </td>
<td>28th </td>
<td>29th</td>
<td bgcolor="#CCCCCC">30th </td>
<td bgcolor="#4357CFF">1st December </td>
</tr>
<tr valign="top">
<td>2nd </td>
<td>3rd </td>
<td>4th </td>
<td>5th </td>
<td>6th</td>
<td bgcolor="#CCCCCC">7th </td>
<td bgcolor="#CCCCCC">8th </td>
</tr>
<tr valign="top">
<td>9th </td>
<td>10th </td>
<td>11th </td>
<td>12th </td>
<td bgcolor="#FFA500">13th '''End of term'''</td>
<td bgcolor="#CCCCCC">14th </td>
<td bgcolor="#CCCCCC">15th </td>
</tr>
<tr valign="top">
<td>16th </td>
<td>17th </td>
<td>18th </td>
<td>19th </td>
<td>20th </td>
<td bgcolor="#CCCCCC">21st </td>
<td bgcolor="#CCCCCC">22nd </td>
</tr>
<tr valign="top">
<td bgcolor="#228B22">23rd '''College closed'''</td>
<td bgcolor="#228B22">24th '''College closed'''</td>
<td bgcolor="#228B22">25th '''College closed'''</td>
<td bgcolor="#228B22">26th '''College closed'''</td>
<td bgcolor="#228B22">27th '''College closed'''</td>
<td bgcolor="#228B22">28th '''College closed'''</td>
<td bgcolor="#228B22">29th '''College closed'''</td>
</tr>
<tr valign="top">
<td bgcolor="#228B22">30th '''College closed'''</td>
<td bgcolor="#228B22">31st '''College closed'''</td>
<td bgcolor="#228B22">1st January '''College closed'''</td>
<td>2nd </td>
<td>3rd Gabriel & Vincent - Science Communication Course</td>
<td bgcolor="#CCCCCC">4th Gabriel & Vincent - Science Communication Course</td>
<td bgcolor="#CCCCCC">5th Gabriel & Vincent - Science Communication Course</td>
</tr>
</table>

Talk:Mod:Hunt Research Group/QMMM SP Aqeuous Cu(II)

2013-10-01T08:00:49Z

Vhc08:

== QM/MM Single Point Energy Calculation of Cu(II) and 2 Solvation Shells ==
In this example, the first solvation shell is modelled at the B3LYP 6-311G level (via Gaussian) while the second solvation shell is modelled using a classical pairwise potential (via DL_POLY). ChemShell employs an additive scheme to calculate the total QM/MM energy i.e. the total energy is the sum of the MM energy of the MM region and the QM energy of the QM region. In addition, link atoms are placed along the axis of bonds at the QM-MM boundary. More details can be found [http://www.cse.scitech.ac.uk/ccg/software/chemshell/manual/hyb_new.html here].

Create an input file called <code>energy.chm</code> with the following content:
<pre>

energy energy=e coords=cu_18water.pun \
theory= hybrid : { coupling=shift
qm_region = {1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22}
qm_theory=gaussian : { basis=6-311g g98_mem=80000000 charge=2 mult=2 hamiltonian=b3lyp}
mm_theory=dl_poly : mm_defs=ff.dat
}
</pre>

The co-ordinates of the system are read from <code>cu_18water.pun</code> (created [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/ChemShell_System_Aqeuous_Cu(II) here]).
The first 22 atoms (Cu(II) + 7 waters in the first solvation shell) are modelled at the B3LYP 6-311G level.
The rest of the system is modelled using the force field defined in <code>ff.dat</code> (see [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/ChemShell_Force_Field_Parameters_Aqueous_Cu(II) here] for details).
The QM and MM regions are coupled via the charge shift scheme.

The calculation should be submitted to the PBS queue to avoid overloading the login shell and inconveniencing other cx1 users (details [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/ChemShell_Introduction here]). Don't forget to load the DL_POLY and Gaussian modules in your submit script!

The energy can be found at the end of the output (<code>energy.out</code>):
<pre>
-----------------------------------------------------------------------------------
Energy ( hybrid): -2175.199009 (a.u.)
-----------------------------------------------------------------------------------
ChemShell exiting code 0
</pre>

Talk:Mod:Hunt Research Group/ChemShell Introduction

2013-10-01T07:59:40Z

Vhc08:

This tutorial will outline the basics of ChemShell leading to a QM/MM calculation of copper(II) and 2 solvation shells.

ChemShell inputs are written in Tcl (Tool Command Language) can be run either interactively or as a script on cx1.

To run ChemShell commands on the login shell, you will need to first load the ChemShell module at the login shell after logging in to cx1:
<pre>
module load chemshell/3.5.0
</pre>
The interactive mode is then invoked by entering <code>chemsh.x</code>.
Alternatively, you can run scripts via the command:
<pre>
chemsh.x NAME_OF_SCRIPT
</pre>
where <code>NAME_OF_SCRIPT</code> is the name of script containing the ChemShell commands you want to run.

==Submitting via the Portable Batch System (PBS)==
To ensure that you are not hogging computing resources on the login shell and inconveniencing other cx1 users, it is best to run your calculations (except the most basic calculations/actions) by submitting to the Portable Batch System (PBS).

A typical submit script will look like the following:

<pre>
#/bin/sh
#PBS -l walltime=48:00:00
#PBS -l mem=2600MB
#PBS -j oe

module load chemshell/3.5.0
module load intel-suite mpi

cp $PBS_O_WORKDIR/energy.chm $TMPDIR
cp $PBS_O_WORKDIR/ff.dat $TMPDIR
cp $PBS_O_WORKDIR/cu_18water.pun $TMPDIR

cd $TMPDIR
mpiexec chemsh.x energy.chm > energy.out

cp $TMPDIR/* $PBS_O_WORKDIR/
</pre>

The command <code>module load chemshell/3.5.0</code> loads the ChemShell module as explained above.
The command <code>module load intel-suite mpi</code> loads the modules which will allow you to run calculations employing more than one processor.

You will also have to load modules of the QM or MM codes that you intend to use during the calculation.

The following <code>cp</code> commands copies all the input files into the temporary directory (<code>$TMPDIR</code>) for running the calculation.

The command <code>mpiexec chemsh.x energy.chm > energy.out</code> instructs ChemShell to execute the script called <code>energy.chm</code> and to write any standard output into <code>energy.out</code>.

The final <code>cp</code> command copies all output files (includes <code>energy.out</code> along with others) back into your working directory at the end.

To submit a script like this into the PBS queue, enter the following at the command line:
<pre>
qsub NAME_OF_SCRIPT
</pre>
where <code>NAME_OF_SCRIPT</code> is the name of the script.

Talk:Mod:Hunt Research Group/QMMM SP Aqeuous Cu(II)

2013-10-01T07:56:10Z

Vhc08:

== QM/MM Single Point Energy Calculation of Cu(II) and 2 Solvation Shells ==
In this example, the first solvation shell is modelled at the B3LYP 6-311G level (via Gaussian) while the second solvation shell is modelled using a classical pairwise potential (via DL_POLY). ChemShell employs an additive scheme to calculate the total QM/MM energy i.e. the total energy is the sum of the MM energy of the MM region and the QM energy of the QM region. In addition, link atoms are placed along the axis of bonds at the QM-MM boundary. More details can be found [http://www.cse.scitech.ac.uk/ccg/software/chemshell/manual/hyb_new.html here].

Create an input file called <code>energy.chm</code> with the following content:
<pre>

energy energy=e coords=cu_18water.pun \
theory= hybrid : { coupling=shift
qm_region = {1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22}
qm_theory=gaussian : { basis=6-311g g98_mem=80000000 charge=2 mult=2 hamiltonian=b3lyp}
mm_theory=dl_poly : mm_defs=ff.dat
}
</pre>

The co-ordinates of the system are read from <code>cu_18water.pun</code> (created [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/ChemShell_System_Aqeuous_Cu(II) here]).
The first 22 atoms (Cu(II) + 7 waters in the first solvation shell) are modelled at the B3LYP 6-311G level.
The rest of the system is modelled using the force field defined in <code>ff.dat</code> (see [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/ChemShell_Force_Field_Parameters_Aqueous_Cu(II) here] for details).
The QM and MM regions are coupled via the charge shift scheme.

The calculation should be submitted to the PBS queue to avoid overloading the login shell and inconveniencing other cx1 users (details [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/ChemShell_Introduction here]).

The energy can be found at the end of the output (<code>energy.out</code>):
<pre>
-----------------------------------------------------------------------------------
Energy ( hybrid): -2175.199009 (a.u.)
-----------------------------------------------------------------------------------
ChemShell exiting code 0
</pre>

Talk:Mod:Hunt Research Group/QMMM SP Aqeuous Cu(II)

2013-10-01T07:55:54Z

Vhc08:

== QM/MM Single Point Energy Calculation of Cu(II) and 2 Solvation Shells ==
In this example, the first solvation shell is modelled at the B3LYP 6-311G level (via Gaussian) while the second solvation shell is modelled using a classical pairwise potential (via DL_POLY). ChemShell employs an additive scheme to calculate the total QM/MM energy i.e. the total energy is the sum of the MM energy of the MM region and the QM energy of the QM region. In addition, link atoms are placed along the axis of bonds at the QM-MM boundary. More details can be found [here http://www.cse.scitech.ac.uk/ccg/software/chemshell/manual/hyb_new.html].

Create an input file called <code>energy.chm</code> with the following content:
<pre>

energy energy=e coords=cu_18water.pun \
theory= hybrid : { coupling=shift
qm_region = {1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22}
qm_theory=gaussian : { basis=6-311g g98_mem=80000000 charge=2 mult=2 hamiltonian=b3lyp}
mm_theory=dl_poly : mm_defs=ff.dat
}
</pre>

The co-ordinates of the system are read from <code>cu_18water.pun</code> (created [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/ChemShell_System_Aqeuous_Cu(II) here]).
The first 22 atoms (Cu(II) + 7 waters in the first solvation shell) are modelled at the B3LYP 6-311G level.
The rest of the system is modelled using the force field defined in <code>ff.dat</code> (see [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/ChemShell_Force_Field_Parameters_Aqueous_Cu(II) here] for details).
The QM and MM regions are coupled via the charge shift scheme.

The calculation should be submitted to the PBS queue to avoid overloading the login shell and inconveniencing other cx1 users (details [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/ChemShell_Introduction here]).

The energy can be found at the end of the output (<code>energy.out</code>):
<pre>
-----------------------------------------------------------------------------------
Energy ( hybrid): -2175.199009 (a.u.)
-----------------------------------------------------------------------------------
ChemShell exiting code 0
</pre>

Talk:Mod:Hunt Research Group/QMMM SP Aqeuous Cu(II)

2013-10-01T07:55:39Z

Vhc08:

== QM/MM Single Point Energy Calculation of Cu(II) and 2 Solvation Shells ==
In this example, the first solvation shell is modelled at the B3LYP 6-311G level (via Gaussian) while the second solvation shell is modelled using a classical pairwise potential (via DL_POLY). ChemShell employs an additive scheme to calculate the total QM/MM energy i.e. the total energy is the sum of the MM energy of the MM region and the QM energy of the QM region. In addition, link atoms are placed along the axis of bonds at the QM-MM boundary. More details can be found [http://www.cse.scitech.ac.uk/ccg/software/chemshell/manual/hyb_new.html].

Create an input file called <code>energy.chm</code> with the following content:
<pre>

energy energy=e coords=cu_18water.pun \
theory= hybrid : { coupling=shift
qm_region = {1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22}
qm_theory=gaussian : { basis=6-311g g98_mem=80000000 charge=2 mult=2 hamiltonian=b3lyp}
mm_theory=dl_poly : mm_defs=ff.dat
}
</pre>

The co-ordinates of the system are read from <code>cu_18water.pun</code> (created [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/ChemShell_System_Aqeuous_Cu(II) here]).
The first 22 atoms (Cu(II) + 7 waters in the first solvation shell) are modelled at the B3LYP 6-311G level.
The rest of the system is modelled using the force field defined in <code>ff.dat</code> (see [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/ChemShell_Force_Field_Parameters_Aqueous_Cu(II) here] for details).
The QM and MM regions are coupled via the charge shift scheme.

The calculation should be submitted to the PBS queue to avoid overloading the login shell and inconveniencing other cx1 users (details [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/ChemShell_Introduction here]).

The energy can be found at the end of the output (<code>energy.out</code>):
<pre>
-----------------------------------------------------------------------------------
Energy ( hybrid): -2175.199009 (a.u.)
-----------------------------------------------------------------------------------
ChemShell exiting code 0
</pre>

Mod:Hunt Research Group/calendar

2013-09-30T09:51:25Z

Vhc08:

== Calendar ==

*Tricia (Done)
*Abdihakim Hassan (Not Done)
*Bryan Ward (Not Done)
*Claire Ashworth (Not Done)
*Matthew Clough (Done)
*Precious Ugbomah (Done)
*Richard Matthews (Done)
*Vincent Chen (Done)
*Gabriel Lau (Done)
*Sarah Smith (Not Done)

{| class="wikitable" border="1" style="text-align:center"
|+ Theory Group Meetings: 2-3.30pm every other Thursday
!Meeting !! Topic || Name || Date
|-
| <s>1</s> || <s>Differentiation and Integration</s> || Matthew || <s>20th June</s>
|-
| <s>2</s> || <s>Differential Equations</s> || Claire || <s>27th</s> <s>June</s>
|-
| 3|| <s>Matrix Mechanics</s> ||Gabriel|| <s>1st August</s>
|-
| 4 || Linear Algebra || Richard || Postponed
|-
| 5 || Chem. I - topic TBD ||Bryan || Postponed
|-
| 6 ||Perturbation Theory|| Vincent|| Postponed
|}

<table border="1" cellpadding="5" width="1190">
<tr bgcolor="#66CCFF">
<th width="170px">Mon</th>
<th width="170px">Tues</th>
<th width="170px">Wed</th>
<th width="170px">Thur</th>
<th width="170px">Fri</th>
<th width="170px" bgcolor="#CCCCCC">Sat</th>
<th width="170px" bgcolor="#CCCCCC">Sun</th>
<tr valign="top">
<td>16th </td>
<td>17th Bryan/Claire - Gaussian Workshop</td>
<td>18th Bryan/Claire - Gaussian Workshop</td>
<td>19th </td>
<td>20th '''(Sarah)'''</td>
<td bgcolor="#CCCCCC">21st </td>
<td bgcolor="#CCCCCC">22nd </td>
</tr>
<tr valign="top">
<td>23rd </td>
<td>24th </td>
<td>25th </td>
<td>26th </td>
<td>27th Claire away</td>
<td bgcolor="#FFA500">28th '''Start of Term'''</td>
<td bgcolor="#CCCCCC">29th </td>
</tr>
<tr valign="top">
<td>30th Claire away</td>
<td bgcolor="#4357CFF">1st October '''(Paper)''' Claire away</td>
<td>2nd Claire away</td>
<td>3rd Claire away</td>
<td>4th Claire away </td>
<td bgcolor="#CCCCCC">5th </td>
<td bgcolor="#CCCCCC">6th </td>
</tr>
<tr valign="top">
<td>7th </td>
<td>8th '''(Precious)'''</td>
<td>9th </td>
<td>10th '''Theory Meeting'''</td>
<td>11th </td>
<td bgcolor="#CCCCCC">12th </td>
<td bgcolor="#CCCCCC">13th </td>
</tr>
<tr valign="top">
<td>14th </td>
<td>15th '''(Claire)'''</td>
<td>16th </td>
<td>17th </td>
<td>18th </td>
<td bgcolor="#CCCCCC">19th </td>
<td bgcolor="#CCCCCC">20th </td>
</tr>
<tr valign="top">
<td>21st </td>
<td>22nd '''(Bryan)'''</td>
<td>23rd </td>
<td>24th </td>
<td>25th </td>
<td bgcolor="#CCCCCC">26th </td>
<td bgcolor="#CCCCCC">27th </td>
</tr>
<tr valign="top">
<td>28th </td>
<td>29th '''(Matthew)'''</td>
<td>30th </td>
<td>31st </td>
<td bgcolor="#4357CFF">1st November </td>
<td bgcolor="#CCCCCC">2nd </td>
<td bgcolor="#CCCCCC">3rd </td>
</tr>
<tr valign="top">
<td>4th </td>
<td>5th '''(Vincent)'''</td>
<td>6th </td>
<td>7th </td>
<td>8th</td>
<td bgcolor="#CCCCCC">9th </td>
<td bgcolor="#CCCCCC">10th </td>
</tr>
<tr valign="top">
<td>11th </td>
<td>12th '''(Gabriel)'''</td>
<td>13th </td>
<td>14th </td>
<td>15th</td>
<td bgcolor="#CCCCCC">16th </td>
<td bgcolor="#CCCCCC">17th </td>
</tr>
<tr valign="top">
<td>18th </td>
<td>19th </td>
<td>20th </td>
<td>21st </td>
<td>22nd</td>
<td bgcolor="#CCCCCC">23rd </td>
<td bgcolor="#CCCCCC">24th </td>
</tr>
<tr valign="top">
<td>25th </td>
<td>26th </td>
<td>27th </td>
<td>28th </td>
<td>29th</td>
<td bgcolor="#CCCCCC">30th </td>
<td bgcolor="#4357CFF">1st December </td>
</tr>
<tr valign="top">
<td>2nd </td>
<td>3rd </td>
<td>4th </td>
<td>5th </td>
<td>6th</td>
<td bgcolor="#CCCCCC">7th </td>
<td bgcolor="#CCCCCC">8th </td>
</tr>
<tr valign="top">
<td>9th </td>
<td>10th </td>
<td>11th </td>
<td>12th </td>
<td bgcolor="#FFA500">13th '''End of term'''</td>
<td bgcolor="#CCCCCC">14th </td>
<td bgcolor="#CCCCCC">15th </td>
</tr>
<tr valign="top">
<td>16th </td>
<td>17th </td>
<td>18th </td>
<td>19th </td>
<td>20th </td>
<td bgcolor="#CCCCCC">21st </td>
<td bgcolor="#CCCCCC">22nd </td>
</tr>
<tr valign="top">
<td bgcolor="#228B22">23rd '''College closed'''</td>
<td bgcolor="#228B22">24th '''College closed'''</td>
<td bgcolor="#228B22">25th '''College closed'''</td>
<td bgcolor="#228B22">26th '''College closed'''</td>
<td bgcolor="#228B22">27th '''College closed'''</td>
<td bgcolor="#228B22">28th '''College closed'''</td>
<td bgcolor="#228B22">29th '''College closed'''</td>
</tr>
<tr valign="top">
<td bgcolor="#228B22">30th '''College closed'''</td>
<td bgcolor="#228B22">31st '''College closed'''</td>
<td bgcolor="#228B22">1st January '''College closed'''</td>
<td>2nd </td>
<td>3rd</td>
<td bgcolor="#CCCCCC">4th </td>
<td bgcolor="#CCCCCC">5th </td>
</tr>
</table>

Talk:Mod:Hunt Research Group/ChemShell Introduction

2013-09-13T15:17:09Z

Vhc08:

This tutorial will outline the basics of ChemShell leading to a QM/MM calculation of copper(II) and 2 solvation shells.

ChemShell inputs are written in Tcl (Tool Command Language) can be run either interactively or as a script on cx1.

To run ChemShell commands on the login shell, you will need to first load the ChemShell module at the login shell after logging in to cx1:
<pre>
module load chemshell/3.5.0
</pre>
The interactive mode is then invoked by entering <code>chemsh.x</code>.
Alternatively, you can run scripts via the command:
<pre>
chemsh.x NAME_OF_SCRIPT
</pre>
where <code>NAME_OF_SCRIPT</code> is the name of script containing the ChemShell commands you want to run.

==Submitting via the Portable Batch System (PBS)==
To ensure that you are not hogging computing resources on the login shell and inconveniencing other cx1 users, it is best to run your calculations (except the most basic calculations/actions) by submitting to the Portable Batch System (PBS).

A typical submit script will look like the following:

<pre>
#/bin/sh
#PBS -l walltime=48:00:00
#PBS -l mem=2600MB
#PBS -j oe

module load chemshell/3.5.0
module load intel-suite mpi

cp $PBS_O_WORKDIR/energy.chm $TMPDIR
cp $PBS_O_WORKDIR/ff.dat $TMPDIR
cp $PBS_O_WORKDIR/cu_18water.pun $TMPDIR

cd $TMPDIR
mpiexec chemsh.x energy.chm > energy.out

cp $TMPDIR/* $PBS_O_WORKDIR/
</pre>

The command <code>module load chemshell/3.5.0</code> loads the ChemShell module as explained above.
The command <code>module load intel-suite mpi</code> loads the modules which will allow you to run calculations employing more than one processor.

The following <code>cp</code> commands copies all the input files into the temporary directory (<code>$TMPDIR</code>) for running the calculation.

The command <code>mpiexec chemsh.x energy.chm > energy.out</code> instructs ChemShell to execute the script called <code>energy.chm</code> and to write any standard output into <code>energy.out</code>.

The final <code>cp</code> command copies all output files (includes <code>energy.out</code> along with others) back into your working directory at the end.

To submit a script like this into the PBS queue, enter the following at the command line:
<pre>
qsub NAME_OF_SCRIPT
</pre>
where <code>NAME_OF_SCRIPT</code> is the name of the script.

Talk:Mod:Hunt Research Group/QMMM MD Aqeuous Cu(II)

2013-09-11T14:25:43Z

Vhc08:

Talk:Mod:Hunt Research Group/QMMM MD Aqeuous Cu(II)

2013-09-11T14:25:32Z

Vhc08:

Talk:Mod:Hunt Research Group/QMMM MD Aqeuous Cu(II)

2013-09-11T14:21:25Z

Vhc08:

Talk:Mod:Hunt Research Group/QMMM MD Aqeuous Cu(II)

2013-09-11T14:19:42Z

Vhc08:

This input runs a short 0.1 ps (timestep = 0.001 ps) QM/MM molecular dynamics simulation of an [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/ChemShell_System_Aqeuous_Cu(II) aqueous copper system].
<pre>
#
# Create the dynamics object
#
dynamics dyn1 coords=cu_18water_qmmm_opt.pun \
theory= hybrid : { coupling=shift qm_region = {1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22} \
qm_theory=gaussian : { nproc=8 basis=6-311g g98_mem=80000000 charge=2 mult=2 hamiltonian=b3lyp } \
mm_theory=dl_poly : mm_defs=ff.dat } timestep = 0.001 ensemble = NVE

# initialise random velocities
dyn1 initvel
dyn1 output
#
set count 0
while {$count < 100} {

# Update MM pairlist every 10 steps
if { [ expr $count % 10 ] == 0 } { dyn1 update }
dyn1 force

# output the coordinates to the trajectory every 50 steps
if { [ expr $count % 10 ] == 0 } { dyn1 trajectory }

dyn1 printe
dyn1 step
incr count
}

dyn1 destroy

times

</pre>

The initial configuration is taken from the [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/QMMM_OPT_Aqeuous_Cu(II) QM/MM optimisation].
To run this, login to cx1 and submit this simulation into the PBS queue.

'''NB: When I ran this simulation, ChemShell was throwing weird errors. It only worked when I put the code defining the dynamics object <code>dyn1</code> into a single line.'''

The simulation will take a while (~ 1 hour). Once finished, you should see <code>md.out</code> and <code>dynamics.trj</code> in your working directory.
If there were no errors, the end of <code>md.out</code> should look something like this:

<pre>
Energy and gradient evaluations:
QM energies 100
QM gradients 100
MM energies 100
MM gradients 100

Timing Analysis by Executable
g09 [ 100] 3659.293 99.9%
ChemShell 2.041 0.1%

Total 3661.334

Timing Analysis by Module module # calls time time (exc) percent
dynamics [ 1] 3661.144 0.057 0.0%
hybrid.kill [ 1] 0.001 0.001 0.0%
dl_poly.kill [ 1] 0.000 0.000 0.0%
hybrid.calc [ 100] 3661.024 0.038 0.0%
dl_poly.eandg [ 100] 0.237 0.237 0.0%
gaussian [ 100] 3660.750 3660.342 100.0%
set_matrix_element [ 16600] 0.147 0.147 0.0%
set_matrix_size [ 200] 0.005 0.005 0.0%
get_bq_entry [ 6600] 0.084 0.084 0.0%
get_ecp [ 100] 0.116 0.074 0.0%
get_element_data [ 2200] 0.014 0.014 0.0%
hybrid.update [ 10] 0.015 0.003 0.0%
dl_poly.update [ 10] 0.011 0.011 0.0%
hybrid.init [ 1] 0.047 0.031 0.0%
dl_poly.init [ 1] 0.016 0.016 0.0%
get_cell [ 1] 0.000 0.000 0.0%
connect [ 1] 0.000 0.000 0.0%
get_number_of_bqs [ 101] 0.002 0.002 0.0%
get_number_of_shells [ 3] 0.000 0.000 0.0%
get_connected_atoms [ 22] 0.000 0.000 0.0%
get_atom_entry [ 6622] 0.080 0.080 0.0%
copy_object [ 1] 0.000 0.000 0.0%
check_molecule_connectivity [ 2] 0.000 0.000 0.0%
get_number_of_atoms [ 303] 0.003 0.003 0.0%
Other 0.190 0.0%

Total 3661.334
ChemShell exiting code 0
</pre>

<code>dynamics.traj</code> contains the trajectory of the MD run. It should look something like this:
<pre>
block=fragment.sequence records=0
block=coordinates records=55
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o -0.083576 0.762461 0.928069
h 1.218317 1.880815 0.130918
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o -4.519530 8.778483 1.467508
h -3.493799 10.307577 1.112111
h -5.550743 8.252819 -0.019924
o -4.954629 8.710028 6.836740
h -4.055333 10.155954 7.499569
h -6.873509 8.634215 6.958246
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h 0.014980 9.552512 5.903353
o -4.017236 3.618939 1.749376
h -2.589665 2.446039 1.364619
h -5.667027 3.098309 1.074914
o -3.391765 3.793140 6.748087
h -3.252752 4.173894 8.580987
h -3.617533 1.969201 6.371438
o 4.886245 7.323613 3.035603
h 5.905049 6.260575 4.237513
h 5.978293 8.776280 2.481551
o -4.300274 -2.369841 0.855820
h -4.483208 -4.022556 -0.059603
h -2.774842 -1.457930 0.159943
o -11.518225 3.917079 9.096873
h -13.144578 4.046564 10.068526
h -10.863967 2.152758 9.329397
o -0.727844 11.891304 8.165890
h -0.033099 11.711029 9.926526
h -0.686281 13.736744 7.717125
o -2.027565 12.794421 0.060931
h -2.596210 14.596843 0.241231
h -0.659816 12.750215 -1.255099
o -3.946933 -0.998968 5.756755
h -4.255971 -1.525974 3.942783
h -4.006754 -2.575590 6.812611
o -13.042960 9.805782 3.784247
h -14.894201 9.812855 4.206000
h -12.776118 11.039863 2.368998
o 3.187058 3.988931 -0.702261
h 4.044622 4.311740 -2.362579
h 3.808139 5.301715 0.531815
o -7.348413 7.182890 -2.191777
h -8.066059 5.506379 -1.635472
h -7.986743 7.543168 -3.941897
o -8.740894 2.672050 0.204944
h -9.210936 1.053651 -0.672238
h -10.118628 3.056161 1.452498
o -3.090669 4.634024 11.606310
h -4.361408 5.675073 12.555488
h -1.858357 3.926491 12.864479
block=update_coordinates records=55
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o -0.108291 0.662057 0.875603
h 1.092434 1.823054 -0.012381
h 0.627664 0.030774 2.426616
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h -3.431835 10.206983 1.094289
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h -4.111675 10.210162 7.668491
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o -9.448665 7.685461 6.340187
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o 0.085853 8.206543 4.709663
h 1.766433 8.007057 3.966225
h 0.046867 9.572561 5.956115
o -4.029740 3.586616 1.719834
h -2.593939 2.413401 1.398341
h -5.662705 3.028327 1.047417
o -3.424548 3.720787 6.727423
h -3.250861 4.121120 8.551552
h -3.779189 1.917627 6.378730
o 4.995600 7.367619 3.005797
h 6.008234 6.186735 4.094361
h 6.206435 8.666970 2.315186
o -4.363873 -2.437806 0.960948
h -4.448308 -4.171186 0.167384
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o -11.423871 3.700929 8.978197
h -12.947247 3.918002 10.049199
h -10.751475 1.952781 9.341881
o -0.514082 12.112154 8.287439
h 0.199786 11.966829 10.068623
h -0.441351 13.994396 8.003580
o -1.970013 12.709458 0.040809
h -2.568429 14.494590 0.244146
h -0.555362 12.687158 -1.259090
o -3.869360 -1.065867 5.736818
h -4.166092 -1.866178 4.012471
h -4.067672 -2.475658 6.994878
o -13.061802 9.637356 3.877019
h -14.925099 9.634282 4.282584
h -12.774033 10.948868 2.555701
o 3.063029 3.913205 -0.861599
h 4.049648 4.013092 -2.499460
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o -7.172084 7.174326 -2.295341
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h -9.216160 1.127254 -0.908414
h -10.320564 3.069537 1.204719
o -3.268579 4.627503 11.687971
h -4.225436 5.978500 12.669773
h -1.970046 3.930527 12.896909
block=update_coordinates records=55
cu -3.928183 6.616673 4.247312
o -0.151801 0.565973 0.838577
h 0.982422 1.703505 -0.148616
h 0.687065 0.124640 2.404862
o -4.729086 8.914271 1.630579
h -3.628799 10.392190 1.232955
h -5.602758 8.226966 0.120931
o -4.908967 8.865303 6.994093
h -4.013630 10.264525 7.703854
h -6.794329 8.816177 7.075042
o -9.367926 7.696464 6.215730
h -10.833489 8.478328 5.284604
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o 0.143213 8.238687 4.774527
h 1.815074 7.948305 4.031196
h 0.230794 9.622633 5.988555
o -4.049799 3.612015 1.717255
h -2.670109 2.383571 1.391916
h -5.675653 2.982436 1.081677
o -3.467545 3.714949 6.706603
h -3.474639 3.993957 8.565425
h -3.606035 1.919421 6.207665
o 5.090207 7.442653 3.025357
h 6.127731 6.072387 3.813258
h 6.281020 8.452136 1.960412
o -4.429923 -2.502571 0.968120
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o -1.909725 12.602834 0.020547
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o -3.809233 -1.118376 5.790072
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o -13.089247 9.491897 3.947513
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h -4.160275 6.050373 12.732587
h -2.181767 3.766349 12.868630
block=update_coordinates records=55
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h 0.770565 1.705017 -0.200671
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o 2.813512 3.462391 -1.571663
h 1.990596 3.578113 -3.276219
h 4.699153 3.604594 -1.997209
o -6.636930 7.361221 -2.717524
h -7.797876 6.884599 -4.165743
h -5.045780 7.964415 -3.561625
o -8.890322 2.475987 0.074439
h -8.298136 1.667337 -1.534029
h -10.775637 2.226713 0.049582
o -3.832139 4.630736 11.745247
h -4.517789 5.911891 12.919185
h -3.391126 3.104604 12.771187
block=update_coordinates records=55
cu -4.107880 6.701233 4.400509
o -0.324446 0.467452 0.910415
h 1.132454 1.310744 0.106024
h 0.185567 -0.432547 2.422637
o -5.042995 9.093823 1.714888
h -3.814750 10.448540 1.284492
h -6.017316 8.537292 0.248247
o -4.723772 9.180909 7.173857
h -3.905849 10.662156 7.847922
h -6.608362 9.032237 7.311071
o -8.902699 7.260411 6.087015
h -10.340597 8.020680 5.170515
h -9.410069 5.656478 6.922181
o 0.235253 8.391388 4.945149
h 1.953738 8.005124 4.359656
h 0.309393 9.784880 6.155455
o -4.393180 4.017790 1.889032
h -3.093896 2.738713 1.423525
h -6.026233 3.511234 1.134804
o -3.760700 4.138430 6.879422
h -3.682567 4.459956 8.746521
h -3.799550 2.360129 6.463671
o 5.156010 7.593126 3.066044
h 6.733675 7.188783 4.059745
h 5.611848 8.923854 1.782834
o -4.793020 -2.703545 0.708939
h -5.464333 -4.473452 0.688231
h -3.307258 -2.616356 -0.460046
o -10.702551 3.020851 8.267606
h -12.112136 3.843518 9.218009
h -11.009664 1.154441 8.341950
o 0.402314 12.821632 8.672254
h 1.251661 12.710640 10.390029
h 0.528798 14.667285 8.170899
o -1.729679 12.293474 0.007737
h -2.129036 14.158591 0.037444
h -0.213029 12.004518 -1.115707
o -3.506387 -1.062840 6.506918
h -3.248474 -2.461048 5.198304
h -3.682116 -1.933464 8.198064
o -13.389913 9.075150 4.086731
h -14.842571 8.028768 4.703794
h -14.097053 10.643784 3.297397
o 2.765175 3.283784 -1.821955
h 1.629492 4.050789 -3.098464
h 4.561815 3.514707 -2.362065
o -6.458549 7.491881 -2.862398
h -7.819215 7.122461 -4.140669
h -4.769868 7.308247 -3.684285
o -8.831119 2.474503 0.007496
h -8.198270 1.352466 -1.392628
h -10.544903 1.798147 0.493950
o -3.967922 4.590107 11.690918
h -4.578962 5.978935 12.868172
h -3.713942 3.010216 12.750215
block=update_coordinates records=55
cu -4.140627 6.738020 4.417828
o -0.393249 0.567672 0.979045
h 1.067394 1.267161 0.068263
h 0.067233 -0.562162 2.334871
o -5.081244 9.097527 1.798612
h -3.765987 10.373882 1.321271
h -5.700080 8.440475 0.168766
o -4.664560 9.236778 7.182947
h -3.792945 10.733349 7.700736
h -6.539226 9.150479 7.349355
o -8.816594 7.108201 6.073826
h -10.304400 7.879031 5.265130
h -9.232754 5.360757 6.638955
o 0.214193 8.432859 4.959839
h 1.866107 7.864507 4.333411
h 0.395491 9.758875 6.232194
o -4.479224 4.032574 1.890726
h -3.101746 2.837544 1.447303
h -6.193861 3.624456 1.279400
o -3.823410 4.176742 7.031803
h -4.026075 4.488779 8.925811
h -3.593420 2.387362 6.681466
o 5.095822 7.646555 3.095456
h 6.619439 7.476284 4.199716
h 5.478580 8.971395 1.797516
o -4.924525 -2.732357 0.660989
h -5.670990 -4.471924 0.394094
h -3.642177 -2.433553 -0.673305
o -10.559995 2.979913 8.083526
h -11.842717 3.554048 9.344569
h -10.729463 1.071523 7.970919
o 0.546469 12.869720 8.685007
h 1.405239 12.852207 10.378781
h 0.704561 14.657470 8.125347
o -1.704402 12.245796 0.011749
h -1.880233 14.117318 -0.108653
h -0.200898 11.746011 -1.055200
o -3.419715 -0.973852 6.729529
h -3.460658 -2.249025 5.330360
h -3.666800 -1.946628 8.311376
o -13.427609 8.933534 4.135619
h -14.920929 7.868684 4.666944
h -14.119155 10.574889 3.501195
o 2.703136 3.127249 -2.060286
h 1.582375 4.366684 -3.027026
h 4.446930 3.202487 -2.743289
o -6.257004 7.605525 -2.983766
h -7.823227 7.587377 -4.032974
h -4.906679 6.708039 -4.004740
o -8.733014 2.436068 -0.041063
h -8.316474 1.233593 -1.456575
h -10.233186 1.758557 0.892529
o -4.119093 4.537884 11.652393
h -4.482872 6.024298 12.782472
h -3.924253 3.064320 12.809304
block=update_coordinates records=55
cu -4.171093 6.769292 4.448353
o -0.506557 0.712861 1.045502
h 0.831626 1.359392 -0.076871
h 0.148131 -0.532089 2.205525
o -5.063530 9.125185 1.814799
h -3.845241 10.510936 1.439006
h -5.591747 8.320700 0.231810
o -4.620928 9.294125 7.185502
h -3.751904 10.837136 7.573472
h -6.466533 9.217807 7.462269
o -8.732156 6.978363 6.019411
h -10.260922 7.746977 5.299249
h -9.231786 5.340708 6.864796
o 0.170415 8.466091 4.958403
h 1.772561 7.800937 4.271858
h 0.599446 9.679493 6.287313
o -4.515869 4.031997 1.890552
h -3.195802 2.702334 1.657773
h -6.133203 3.339886 1.202165
o -3.878437 4.173392 7.089644
h -4.019662 4.576624 8.977218
h -3.504098 2.368306 6.904119
o 4.993586 7.735110 3.154258
h 6.554282 7.506480 4.211150
h 5.500749 8.799745 1.669889
o -5.069073 -2.751041 0.614257
h -5.874882 -4.390398 0.168941
h -3.874951 -2.257855 -0.802936
o -10.418394 2.921824 7.902575
h -11.506189 3.221600 9.461122
h -10.454072 1.074498 7.548060
o 0.681330 12.899257 8.679916
h 1.484821 12.765518 10.371329
h 0.824175 14.637959 7.929624
o -1.686412 12.189200 0.018623
h -1.678588 14.082930 -0.227505
h -0.211876 11.582568 -0.969724
o -3.349437 -0.861311 6.937678
h -3.688284 -2.004876 5.494317
h -3.513151 -1.890374 8.550083
o -13.436740 8.768321 4.205879
h -15.013066 7.788790 4.549835
h -14.001911 10.510193 3.665949
o 2.628405 2.994826 -2.269583
h 1.860323 4.427191 -3.220075
h 4.316360 2.714364 -3.166663
o -6.045440 7.676649 -3.071707
h -7.667725 8.334927 -3.851491
h -5.302119 6.489554 -4.355681
o -8.599882 2.371492 -0.047834
h -8.710004 1.379421 -1.664479
h -10.132194 1.838379 0.942053
o -4.294849 4.496294 11.696184
h -4.321023 6.097903 12.678001
h -4.046770 3.068007 12.926790
block=update_coordinates records=55
cu -4.203976 6.783462 4.488997
o -0.637732 0.894982 1.099350
h 0.463999 1.615931 -0.208634
h 0.228846 -0.384012 2.064309
o -5.018580 9.158522 1.789800
h -3.818207 10.550875 1.336931
h -5.500209 8.379066 0.170458
o -4.596631 9.354350 7.198676
h -3.757960 10.955495 7.481290
h -6.422786 9.261162 7.478134
o -8.651137 6.911549 5.952904
h -10.149866 7.629591 5.137901
h -9.180426 5.331350 6.888058
o 0.124762 8.478692 4.949102
h 1.706723 7.951398 4.105984
h 0.526538 9.662438 6.307831
o -4.479845 3.990645 1.912432
h -3.059132 2.760485 1.770255
h -6.091356 3.410617 1.143431
o -3.894207 4.161397 7.053216
h -4.067897 4.500054 8.929309
h -3.694534 2.325732 6.769643
o 4.873839 7.844777 3.221619
h 6.412805 7.328706 4.220625
h 5.482688 8.457560 1.524951
o -5.220394 -2.743756 0.562327
h -6.081797 -4.348790 0.051746
h -4.029851 -2.240467 -0.809245
o -10.274257 2.831808 7.766590
h -11.205381 2.806372 9.411054
h -10.348429 1.077303 7.054180
o 0.789908 12.881436 8.633599
h 1.596745 12.885243 10.376148
h 1.094207 14.656055 7.982194
o -1.663607 12.147486 0.022935
h -1.666542 14.037181 -0.241379
h -0.181141 11.383353 -0.907132
o -3.302079 -0.722877 7.139526
h -3.874803 -1.910435 5.732136
h -3.142060 -1.782400 8.717904
o -13.417703 8.593015 4.295430
h -15.079548 7.684947 4.376878
h -13.750652 10.389143 3.803444
o 2.561212 2.880228 -2.474508
h 2.099857 4.362694 -3.519061
h 3.975716 1.928224 -3.291030
o -5.872852 7.727295 -3.130633
h -7.050137 9.140447 -3.624026
h -5.628535 6.584216 -4.606642
o -8.493257 2.264208 -0.045587
h -8.890287 1.903197 -1.872689
h -10.125387 2.074740 0.911374
o -4.465847 4.478702 11.821631
h -4.224833 6.144650 12.748340
h -4.274074 3.071543 13.114549
</pre>

Talk:Mod:Hunt Research Group/QMMM MD Aqeuous Cu(II)

2013-09-11T14:18:15Z

Vhc08:

Talk:Mod:Hunt Research Group/QMMM OPT Aqeuous Cu(II)

2013-09-11T12:17:11Z

Vhc08:

This ChemShell code runs a QM/MM geometry optimisation on our copper(II)-water system:

<pre>
newopt function = copt : { coords=cu_18water.pun
theory= hybrid : { coupling=shift
qm_region = {1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22}
qm_theory=gaussian : { basis=6-311g g98_mem=80000000 charge=2 mult=2 hamiltonian=b3lyp }
mm_theory=dl_poly : mm_defs=ff.dat
}
result=cu_18water_qmmm_opt.pun
}
</pre>

The <code>newopt</code> command invokes a general purpose optimiser code. The target function <code>copt</code> carries out the optimisation in Cartesian co-ordinates.

The initial co-ordinates are taken from [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/ChemShell_System_Aqeuous_Cu(II) here] while the force field parameters were defined [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/QMMM_SP_Aqeuous_Cu(II) here].

To run the optimisation, login to cx1 and submit the code via the PBS queue system (details [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/ChemShell_Introduction here]).
If the optimisation is successful, you should see something like this at the end of the <code>.out</code> file:
<pre>
--------------------------------------------------------------------------------
********************************************************************************
Optimisation finished successfully
********************************************************************************
Results have been written to cu_18water_qmmm_opt.pun
newopt/copt/===================================== Tstep: 0.0 Ttot:42371.2 ==
newopt/copt/hybrid.kill/========================= Tstep: 0.0 Ttot:42371.2 ==
...hybrid.kill/dl_poly.kill/===================== Tstep: 0.0 Ttot:42371.2 ==

******************************* DL_POLY finished *******************************

MM termination code: 0
Energy and gradient evaluations:
QM energies 203
QM gradients 203
MM energies 203
MM gradients 203
no: end of optimisation
ChemShell exiting code 0
</pre>

The optimised structure is outputted into <code>cu_18water_qmmm_opt.pun</code>, which should look something like this:
<pre>
block = fragment records = 0
block = title records = 1
molecule 1
block = coordinates records = 55
cu -3.76257780766541e+00 6.39581622755847e+00 4.18666084467700e+00
o -8.61211193402496e-02 7.64015048162733e-01 9.28566236359741e-01
h 1.21543269728197e+00 1.88270779646951e+00 1.31175606629519e-01
h 6.37781706300753e-01 -7.82734221778962e-02 2.38728556418122e+00
o -4.51642283433391e+00 8.77759819691374e+00 1.46678151077030e+00
h -3.49172990884007e+00 1.03072164818830e+01 1.11089581484648e+00
h -5.54866802060477e+00 8.25158794461243e+00 -1.97852968619387e-02
o -4.95471761998812e+00 8.71052570690642e+00 6.83662498793940e+00
h -4.05605484296627e+00 1.01570572540756e+01 7.49895970199808e+00
h -6.87371317404838e+00 8.63461596505159e+00 6.95816954313609e+00
o -9.51480700603425e+00 7.65268168973318e+00 6.49527652838249e+00
h -1.08191880350448e+01 8.52142478395586e+00 5.45922246856226e+00
h -1.02602478290014e+01 6.29462819566987e+00 7.55178619381274e+00
o 1.21783543029695e-02 8.18965965674802e+00 4.64643593288696e+00
h 1.70179143020656e+00 7.88361340447555e+00 3.95575265334706e+00
h 1.53560458819001e-02 9.55384358956816e+00 5.90422029240048e+00
o -4.02073293122077e+00 3.61793980085322e+00 1.74997219960407e+00
h -2.59371465606442e+00 2.44468654734398e+00 1.36433254970553e+00
h -5.67098509457942e+00 3.09821229178831e+00 1.07603574755595e+00
o -3.38985817557272e+00 3.79310802899656e+00 6.74770649250538e+00
h -3.25082227534437e+00 4.17399732561277e+00 8.58047932923543e+00
h -3.61597049183051e+00 1.96919514808289e+00 6.37114616477612e+00
o 4.88512549227045e+00 7.32303960143179e+00 3.03802690857829e+00
h 5.90371157876586e+00 6.25868175713396e+00 4.23890965743296e+00
h 5.97736349003507e+00 8.77594531470776e+00 2.48511559337944e+00
o -4.29916411874004e+00 -2.37226641024922e+00 8.55602074665862e-01
h -4.48197927494656e+00 -4.02399646204200e+00 -6.12604734180689e-02
h -2.77416381761238e+00 -1.45943015368469e+00 1.60090770859538e-01
o -1.15152916911611e+01 3.91507445983514e+00 9.09487558613262e+00
h -1.31397292921642e+01 4.04276654045411e+00 1.00694432162367e+01
h -1.08607626672630e+01 2.15038777612147e+00 9.32363260523809e+00
o -7.26161532617709e-01 1.18925561409003e+01 8.16570819162541e+00
h -3.38210015169806e-02 1.17120023508492e+01 9.92714273176291e+00
h -6.83632570128503e-01 1.37379782847602e+01 7.71682993448162e+00
o -2.02526336260395e+00 1.27938834288615e+01 5.91933212826634e-02
h -2.59260481593547e+00 1.45962476869073e+01 2.42272907816360e-01
h -6.60720242454038e-01 1.27504221632937e+01 -1.26012417899430e+00
o -3.94420311392931e+00 -9.99442342009302e-01 5.75664862690226e+00
h -4.25433895488514e+00 -1.52750992694953e+00 3.94311845980275e+00
h -4.00360780860933e+00 -2.57522517852673e+00 6.81366036938644e+00
o -1.30415098084718e+01 9.80484470829646e+00 3.78198257557867e+00
h -1.48929394074433e+01 9.81272313216625e+00 4.20334863832536e+00
h -1.27734330674330e+01 1.10379592139561e+01 2.36612507894359e+00
o 3.18343925559676e+00 3.99162245471456e+00 -7.01690759967063e-01
h 4.03998156283156e+00 4.31487863453482e+00 -2.36245736355065e+00
h 3.80617991301159e+00 5.30361078391041e+00 5.32356523409876e-01
o -7.34841503128147e+00 7.18270192875724e+00 -2.19006910801384e+00
h -8.06775536858874e+00 5.50688446733079e+00 -1.63361378230881e+00
h -7.98466645635603e+00 7.54260798655164e+00 -3.94099354583780e+00
o -8.74477062425801e+00 2.67357572335193e+00 2.06916587181714e-01
h -9.21569433472465e+00 1.05523926189405e+00 -6.69813132357446e-01
h -1.01226940595264e+01 3.05868782112006e+00 1.45407977156667e+00
o -3.09052434169466e+00 4.63395423526394e+00 1.16058757972695e+01
h -4.36175688579645e+00 5.67645850057569e+00 1.25528664304173e+01
h -1.86140317121958e+00 3.92461378513185e+00 1.28658799243406e+01
block = connectivity records = 38
1 5
1 17
2 3
2 4
5 6
5 7
8 9
8 10
11 12
11 13
14 15
14 16
17 18
17 19
20 21
20 22
23 24
23 25
26 27
26 28
29 30
29 31
32 33
32 34
35 36
35 37
38 39
38 40
41 42
41 43
44 45
44 46
47 48
47 49
50 51
50 52
53 54
53 55
</pre>

Talk:Mod:Hunt Research Group/QMMM SP Aqeuous Cu(II)

2013-09-11T12:16:36Z

Vhc08:

== QM/MM Single Point Energy Calculation of Cu(II) and 2 Solvation Shells ==
In this example, the first solvation shell is modelled at the B3LYP 6-311G level (via Gaussian) while the second solvation shell is modelled using a classical pairwise potential (via DL_POLY).

Create an input file called <code>energy.chm</code> with the following content:
<pre>

energy energy=e coords=cu_18water.pun \
theory= hybrid : { coupling=shift
qm_region = {1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22}
qm_theory=gaussian : { basis=6-311g g98_mem=80000000 charge=2 mult=2 hamiltonian=b3lyp}
mm_theory=dl_poly : mm_defs=ff.dat
}
</pre>

The co-ordinates of the system are read from <code>cu_18water.pun</code> (created [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/ChemShell_System_Aqeuous_Cu(II) here]).
The first 22 atoms (Cu(II) + 7 waters in the first solvation shell) are modelled at the B3LYP 6-311G level.
The rest of the system is modelled using the force field defined in <code>ff.dat</code> (see [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/ChemShell_Force_Field_Parameters_Aqueous_Cu(II) here] for details).
The QM and MM regions are coupled via the charge shift scheme.

The calculation should be submitted to the PBS queue to avoid overloading the login shell and inconveniencing other cx1 users (details [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/ChemShell_Introduction here]).

The energy can be found at the end of the output (<code>energy.out</code>):
<pre>
-----------------------------------------------------------------------------------
Energy ( hybrid): -2175.199009 (a.u.)
-----------------------------------------------------------------------------------
ChemShell exiting code 0
</pre>

Talk:Mod:Hunt Research Group/ChemShell Introduction

2013-09-11T12:15:49Z

Vhc08:

This tutorial will outline the basics of ChemShell leading to a QM/MM calculation of copper(II) and 2 solvation shells.

ChemShell inputs are written in Tcl (Tool Command Language) can be run either interactively or as a script on cx1.

To run ChemShell commands on the login shell, you will need to first load the ChemShell module at the login shell after logging in to cx1:
<pre>
module load chemshell/3.5.0
</pre>
The interactive mode is then invoked by entering <code>chemsh.x</code>.
Alternatively, you can run scripts via the command:
<pre>
chemsh.x NAME_OF_SCRIPT
</pre>
where <code>NAME_OF_SCRIPT</code> is the name of script containing the ChemShell commands you want to run.

==Submitting via the Portable Batch System (PBS)==
To ensure that you are not hogging computing resources on the login shell and inconveniencing other cx1 users, it is best to run your calculations (except the most basic calculations/actions) by submitting to the Portable Batch System (PBS).

A typical submit script will look like the following:

<pre>
#/bin/sh
#PBS -l walltime=48:00:00
#PBS -l mem=2600MB
#PBS -j oe

module load chemshell/3.5.0

cp $PBS_O_WORKDIR/energy.chm $TMPDIR
cp $PBS_O_WORKDIR/ff.dat $TMPDIR
cp $PBS_O_WORKDIR/cu_18water.pun $TMPDIR

cd $TMPDIR
mpiexec chemsh.x energy.chm > energy.out

cp $TMPDIR/* $PBS_O_WORKDIR/
</pre>

The command <code>module load chemshell/3.5.0</code> loads the ChemShell module as explained above.

The following <code>cp</code> commands copies all the input files into the temporary directory (<code>$TMPDIR</code>) for running the calculation.

The command <code>mpiexec chemsh.x energy.chm > energy.out</code> instructs ChemShell to execute the script called <code>energy.chm</code> and to write any standard output into <code>energy.out</code>.

The final <code>cp</code> command copies all output files (includes <code>energy.out</code> along with others) back into your working directory at the end.

To submit a script like this into the PBS queue, enter the following at the command line:
<pre>
qsub NAME_OF_SCRIPT
</pre>
where <code>NAME_OF_SCRIPT</code> is the name of the script.

Talk:Mod:Hunt Research Group/QMMM MD Aqeuous Cu(II)

2013-09-10T10:51:04Z

Vhc08:

Talk:Mod:Hunt Research Group/QMMM MD Aqeuous Cu(II)

2013-09-10T10:49:47Z

Vhc08:

Mod:Hunt Research Group

2013-09-10T10:39:24Z

Vhc08: /* Running QM/MM Simulations in ChemShell */

==Hunt Group Wiki==

Back to the main [http://www.ch.ic.ac.uk/hunt web-page]
===Resources===
#Computing resources available in the chemistry department [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/computing_resources link]
#HPC servers and run scripts [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/hpc link]

===Visualisation===
*'''ESPs'''
#Instructions for visualizing electrostatic potentials (Gaussview)[https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/electrostatic_potentials link]
#Electrostatic Potentials II (Molden) [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/electrostatic_potentials_2 link]
*'''VMD'''
#Visualising your Simulation [https://www.ch.ic.ac.uk/wiki/index.php/Talk:Mod:Hunt_Research_Group/VisualisingyourSimulation link]
#How to turn a Gaussian optimization into a VMD movie [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/VMDmovie link]
#How to make VMD trajectory repeated periodically [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/vmd link]
*'''JMol'''
#Visualising MOs using Jmol [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:basic_jmol_instructions link]
#Surfaces (Solvent-Accessible and Connolly) in Jmol [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/jmolsurfaces link]
*'''EMO Code'''
#How to use Ling's emo plot code[https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/emoplot link]
#How to plot EMOs [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/emo link]

===Gaussian General===
#A database of common errors encountered when running Gaussian jobs [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/gaussian_errors link]
# [http://www.ch.ic.ac.uk/hunt/g03_man/index.htm G03 Manual]
#How to run NBO5.9 on the HPC [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/NBO5.9 link]
#How to include dispersion [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/dispersion link]
#Basic ONIOM (Mechanical Embedding) [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/basiconiom link]

===Unix and HPC===
#Setting up a connection to HPC if you have a PC [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/hpc_connections link]
#How to fix Windows files under UNIX [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/Windowsfiles link]
#How to make ssh more comfortable [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/pimpSSH link]
#How to set up a SSH keypair [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/SSHkeyfile link]
#How to use gaussview directly on the HPC [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/gview link]
#How to comfortably search through old BASH commands [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/searchbash link]
#How to connect to HPC directory on desktop for file transfers [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/hpc_Directory_on_desktop link]
#How to set up cx2 [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/cx2 link]

===Installing and using packages===
#CPMD: Car-Parrinello Molecular Dynamics [https://www.ch.ic.ac.uk/wiki/index.php/Talk:Mod:Hunt_Research_Group/cpmd link]
#Beginners guide to VMD: a molecular dynamics visualisation package [https://www.ch.ic.ac.uk/wiki/index.php/Talk:Mod:Hunt_Research_Group/vmd link]
#DLPOLY a MD simulation package, Installation on an IMac [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/dlpoly_install link]
#How to install POLYRATE [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/polyrate link]
#How to install Geomview [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/geomview link]
#XMGRACE, gfortran, c compilers for Lion [http://hpc.sourceforge.net/]

===Setup and Running Ab-Initio MD Simulations===
#How to run CPMD to study aqueous solutions [https://www.ch.ic.ac.uk/wiki/index.php/Talk:Mod:Hunt_Research_Group/cpmd_water link]
#How to run CP2K [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/cp2k_how link]
#[bmim]Cl using CPMD [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/bmimCl_cpmd link]
#[bmim]Cl using CP2K [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/bmimCl_cp2k link]
#mman using CPMD and Gaussian [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/mman link]
#[emim]SCN using CP2K[https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/emimscn link]
#CP2K Donts [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/cp2k link]

===Setup and Running Classical MD Simulations===
#DL_POLY FAQs [http://www.stfc.ac.uk/cse/DL_POLY/ccp1gui/38621.aspx] from DL_POLY webpage.
#Packmol for generating starting configurations [http://www.ime.unicamp.br/~martinez/packmol/] from Packmol webpage.
#Getting the Force Field [https://www.ch.ic.ac.uk/wiki/index.php/Talk:Mod:Hunt_Research_Group/Wheretostart link]
#Choosing an Ensemble [https://www.ch.ic.ac.uk/wiki/index.php/Talk:Mod:Hunt_Research_Group/Ensembles link]
#Equilibration and production simulations [https://www.ch.ic.ac.uk/wiki/index.php/Talk:Mod:Hunt_Research_Group/EquilibrationandProduction link]
#Voids in ILs[https://www.ch.ic.ac.uk/wiki/index.php/Talk:Mod:Hunt_Research_Group/voids link]
#How to equilibrate an MD run[https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/equilibration link]
#Equilibration of [bmim][BF4] and [bmim][NO3][https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/BmimBF4_equilibration link]
#Summary of discussions with Ruth[https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/Aug09QtoRuth link]

===Running QM/MM Simulations in ChemShell===
#ChemShell official website which contains the manual and a tutorial [http://www.stfc.ac.uk/CSE/randd/ccg/36254.aspx link]
#Introduction to ChemShell - Copper in water [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/ChemShell_Introduction link]
#Defining the system: Cu2+ and its first 2 solvation shells [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/ChemShell_System_Aqeuous_Cu(II) link]
#Defining the force field parameters [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/ChemShell_Force_Field_Parameters_Aqueous_Cu(II) link]
#Single point QM/MM energy calculation [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/QMMM_SP_Aqeuous_Cu(II) link]
#QM/MM Optimisation [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/QMMM_OPT_Aqeuous_Cu(II) link]
#QM/MM Molecular Dynamics [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/QMMM_MD_Aqeuous_Cu(II) link]

===Research Notes===
#Cl- in water [https://www.ch.ic.ac.uk/wiki/index.php/Talk:Mod:Hunt_Research_Group/wannier_centre link]
#The use of Legendre time correlation functions to study reorientational dynamics in liquids[https://www.ch.ic.ac.uk/wiki/index.php/Talk:Mod:Hunt_Research_Group/legendre link]
#Functional for ILs using CPMD [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/IL_cpmd_functional link]
#Solving the angular part of the Schrödinger equation for a hydrogen atom [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/angular_schrodinger link] (notes by Vincent)

===Admin Stuff===
#Not used to writing a wiki, make your test runs [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/testing on this page]
#How to set-up new macs [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/mac_setup link]
#How to set-up remote desktop [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/mac_remote link]
#[https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/calendar Calendar]
#Demonstrating in the 3rd year computational chemistry lab [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/compchemlab Timetable]
#How to switch the printer HP CP3525dn duplex on and off [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/printing link]

Mod:Hunt Research Group

2013-09-10T10:38:44Z

Vhc08: /* Running QM/MM Simulations in ChemShell */

==Hunt Group Wiki==

Back to the main [http://www.ch.ic.ac.uk/hunt web-page]
===Resources===
#Computing resources available in the chemistry department [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/computing_resources link]
#HPC servers and run scripts [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/hpc link]

===Visualisation===
*'''ESPs'''
#Instructions for visualizing electrostatic potentials (Gaussview)[https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/electrostatic_potentials link]
#Electrostatic Potentials II (Molden) [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/electrostatic_potentials_2 link]
*'''VMD'''
#Visualising your Simulation [https://www.ch.ic.ac.uk/wiki/index.php/Talk:Mod:Hunt_Research_Group/VisualisingyourSimulation link]
#How to turn a Gaussian optimization into a VMD movie [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/VMDmovie link]
#How to make VMD trajectory repeated periodically [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/vmd link]
*'''JMol'''
#Visualising MOs using Jmol [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:basic_jmol_instructions link]
#Surfaces (Solvent-Accessible and Connolly) in Jmol [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/jmolsurfaces link]
*'''EMO Code'''
#How to use Ling's emo plot code[https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/emoplot link]
#How to plot EMOs [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/emo link]

===Gaussian General===
#A database of common errors encountered when running Gaussian jobs [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/gaussian_errors link]
# [http://www.ch.ic.ac.uk/hunt/g03_man/index.htm G03 Manual]
#How to run NBO5.9 on the HPC [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/NBO5.9 link]
#How to include dispersion [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/dispersion link]
#Basic ONIOM (Mechanical Embedding) [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/basiconiom link]

===Unix and HPC===
#Setting up a connection to HPC if you have a PC [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/hpc_connections link]
#How to fix Windows files under UNIX [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/Windowsfiles link]
#How to make ssh more comfortable [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/pimpSSH link]
#How to set up a SSH keypair [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/SSHkeyfile link]
#How to use gaussview directly on the HPC [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/gview link]
#How to comfortably search through old BASH commands [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/searchbash link]
#How to connect to HPC directory on desktop for file transfers [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/hpc_Directory_on_desktop link]
#How to set up cx2 [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/cx2 link]

===Installing and using packages===
#CPMD: Car-Parrinello Molecular Dynamics [https://www.ch.ic.ac.uk/wiki/index.php/Talk:Mod:Hunt_Research_Group/cpmd link]
#Beginners guide to VMD: a molecular dynamics visualisation package [https://www.ch.ic.ac.uk/wiki/index.php/Talk:Mod:Hunt_Research_Group/vmd link]
#DLPOLY a MD simulation package, Installation on an IMac [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/dlpoly_install link]
#How to install POLYRATE [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/polyrate link]
#How to install Geomview [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/geomview link]
#XMGRACE, gfortran, c compilers for Lion [http://hpc.sourceforge.net/]

===Setup and Running Ab-Initio MD Simulations===
#How to run CPMD to study aqueous solutions [https://www.ch.ic.ac.uk/wiki/index.php/Talk:Mod:Hunt_Research_Group/cpmd_water link]
#How to run CP2K [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/cp2k_how link]
#[bmim]Cl using CPMD [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/bmimCl_cpmd link]
#[bmim]Cl using CP2K [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/bmimCl_cp2k link]
#mman using CPMD and Gaussian [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/mman link]
#[emim]SCN using CP2K[https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/emimscn link]
#CP2K Donts [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/cp2k link]

===Setup and Running Classical MD Simulations===
#DL_POLY FAQs [http://www.stfc.ac.uk/cse/DL_POLY/ccp1gui/38621.aspx] from DL_POLY webpage.
#Packmol for generating starting configurations [http://www.ime.unicamp.br/~martinez/packmol/] from Packmol webpage.
#Getting the Force Field [https://www.ch.ic.ac.uk/wiki/index.php/Talk:Mod:Hunt_Research_Group/Wheretostart link]
#Choosing an Ensemble [https://www.ch.ic.ac.uk/wiki/index.php/Talk:Mod:Hunt_Research_Group/Ensembles link]
#Equilibration and production simulations [https://www.ch.ic.ac.uk/wiki/index.php/Talk:Mod:Hunt_Research_Group/EquilibrationandProduction link]
#Voids in ILs[https://www.ch.ic.ac.uk/wiki/index.php/Talk:Mod:Hunt_Research_Group/voids link]
#How to equilibrate an MD run[https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/equilibration link]
#Equilibration of [bmim][BF4] and [bmim][NO3][https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/BmimBF4_equilibration link]
#Summary of discussions with Ruth[https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/Aug09QtoRuth link]

===Running QM/MM Simulations in ChemShell===
#ChemShell official website which contains the manual and a tutorial [http://www.stfc.ac.uk/CSE/randd/ccg/36254.aspx link]
#Introduction to ChemShell - Copper in water [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/ChemShell_Introduction link]
#Defining the system: Cu2+ and its first 2 solvation shells [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/ChemShell_System_Aqeuous_Cu(II) link]
#Defining the force field parameters [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/ChemShell_Force_Field_Parameters_Aqueous_Cu(II) link]
#Single point QM/MM energy calculation [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/QMMM_SP_Aqeuous_Cu(II) link]
#QM/MM Optimisation [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/QMMM_OPT_Aqeuous_Cu(II) link]
#QM/MM Molecular Dynamics [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/QMMM_MD_Aqeuous_Cu(II) link]
<comment>#Submitting ChemShell calculations to cx1 [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/ChemShell_cx1 link]</comment>

===Research Notes===
#Cl- in water [https://www.ch.ic.ac.uk/wiki/index.php/Talk:Mod:Hunt_Research_Group/wannier_centre link]
#The use of Legendre time correlation functions to study reorientational dynamics in liquids[https://www.ch.ic.ac.uk/wiki/index.php/Talk:Mod:Hunt_Research_Group/legendre link]
#Functional for ILs using CPMD [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/IL_cpmd_functional link]
#Solving the angular part of the Schrödinger equation for a hydrogen atom [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/angular_schrodinger link] (notes by Vincent)

===Admin Stuff===
#Not used to writing a wiki, make your test runs [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/testing on this page]
#How to set-up new macs [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/mac_setup link]
#How to set-up remote desktop [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/mac_remote link]
#[https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/calendar Calendar]
#Demonstrating in the 3rd year computational chemistry lab [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/compchemlab Timetable]
#How to switch the printer HP CP3525dn duplex on and off [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/printing link]

Mod:Hunt Research Group

2013-09-10T10:38:26Z

Vhc08: /* Running QM/MM Simulations in ChemShell */

==Hunt Group Wiki==

Back to the main [http://www.ch.ic.ac.uk/hunt web-page]
===Resources===
#Computing resources available in the chemistry department [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/computing_resources link]
#HPC servers and run scripts [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/hpc link]

===Visualisation===
*'''ESPs'''
#Instructions for visualizing electrostatic potentials (Gaussview)[https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/electrostatic_potentials link]
#Electrostatic Potentials II (Molden) [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/electrostatic_potentials_2 link]
*'''VMD'''
#Visualising your Simulation [https://www.ch.ic.ac.uk/wiki/index.php/Talk:Mod:Hunt_Research_Group/VisualisingyourSimulation link]
#How to turn a Gaussian optimization into a VMD movie [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/VMDmovie link]
#How to make VMD trajectory repeated periodically [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/vmd link]
*'''JMol'''
#Visualising MOs using Jmol [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:basic_jmol_instructions link]
#Surfaces (Solvent-Accessible and Connolly) in Jmol [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/jmolsurfaces link]
*'''EMO Code'''
#How to use Ling's emo plot code[https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/emoplot link]
#How to plot EMOs [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/emo link]

===Gaussian General===
#A database of common errors encountered when running Gaussian jobs [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/gaussian_errors link]
# [http://www.ch.ic.ac.uk/hunt/g03_man/index.htm G03 Manual]
#How to run NBO5.9 on the HPC [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/NBO5.9 link]
#How to include dispersion [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/dispersion link]
#Basic ONIOM (Mechanical Embedding) [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/basiconiom link]

===Unix and HPC===
#Setting up a connection to HPC if you have a PC [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/hpc_connections link]
#How to fix Windows files under UNIX [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/Windowsfiles link]
#How to make ssh more comfortable [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/pimpSSH link]
#How to set up a SSH keypair [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/SSHkeyfile link]
#How to use gaussview directly on the HPC [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/gview link]
#How to comfortably search through old BASH commands [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/searchbash link]
#How to connect to HPC directory on desktop for file transfers [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/hpc_Directory_on_desktop link]
#How to set up cx2 [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/cx2 link]

===Installing and using packages===
#CPMD: Car-Parrinello Molecular Dynamics [https://www.ch.ic.ac.uk/wiki/index.php/Talk:Mod:Hunt_Research_Group/cpmd link]
#Beginners guide to VMD: a molecular dynamics visualisation package [https://www.ch.ic.ac.uk/wiki/index.php/Talk:Mod:Hunt_Research_Group/vmd link]
#DLPOLY a MD simulation package, Installation on an IMac [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/dlpoly_install link]
#How to install POLYRATE [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/polyrate link]
#How to install Geomview [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/geomview link]
#XMGRACE, gfortran, c compilers for Lion [http://hpc.sourceforge.net/]

===Setup and Running Ab-Initio MD Simulations===
#How to run CPMD to study aqueous solutions [https://www.ch.ic.ac.uk/wiki/index.php/Talk:Mod:Hunt_Research_Group/cpmd_water link]
#How to run CP2K [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/cp2k_how link]
#[bmim]Cl using CPMD [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/bmimCl_cpmd link]
#[bmim]Cl using CP2K [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/bmimCl_cp2k link]
#mman using CPMD and Gaussian [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/mman link]
#[emim]SCN using CP2K[https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/emimscn link]
#CP2K Donts [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/cp2k link]

===Setup and Running Classical MD Simulations===
#DL_POLY FAQs [http://www.stfc.ac.uk/cse/DL_POLY/ccp1gui/38621.aspx] from DL_POLY webpage.
#Packmol for generating starting configurations [http://www.ime.unicamp.br/~martinez/packmol/] from Packmol webpage.
#Getting the Force Field [https://www.ch.ic.ac.uk/wiki/index.php/Talk:Mod:Hunt_Research_Group/Wheretostart link]
#Choosing an Ensemble [https://www.ch.ic.ac.uk/wiki/index.php/Talk:Mod:Hunt_Research_Group/Ensembles link]
#Equilibration and production simulations [https://www.ch.ic.ac.uk/wiki/index.php/Talk:Mod:Hunt_Research_Group/EquilibrationandProduction link]
#Voids in ILs[https://www.ch.ic.ac.uk/wiki/index.php/Talk:Mod:Hunt_Research_Group/voids link]
#How to equilibrate an MD run[https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/equilibration link]
#Equilibration of [bmim][BF4] and [bmim][NO3][https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/BmimBF4_equilibration link]
#Summary of discussions with Ruth[https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/Aug09QtoRuth link]

===Running QM/MM Simulations in ChemShell===
#ChemShell official website which contains the manual and a tutorial [http://www.stfc.ac.uk/CSE/randd/ccg/36254.aspx link]
#Introduction to ChemShell - Copper in water [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/ChemShell_Introduction link]
#Defining the system: Cu2+ and its first 2 solvation shells [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/ChemShell_System_Aqeuous_Cu(II) link]
#Defining the force field parameters [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/ChemShell_Force_Field_Parameters_Aqueous_Cu(II) link]
#Single point QM/MM energy calculation [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/QMMM_SP_Aqeuous_Cu(II) link]
#QM/MM Optimisation [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/QMMM_OPT_Aqeuous_Cu(II) link]
#QM/MM Molecular Dynamics [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/QMMM_MD_Aqeuous_Cu(II) link]
<nowiki>#Submitting ChemShell calculations to cx1 [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/ChemShell_cx1 link]</nowiki>

===Research Notes===
#Cl- in water [https://www.ch.ic.ac.uk/wiki/index.php/Talk:Mod:Hunt_Research_Group/wannier_centre link]
#The use of Legendre time correlation functions to study reorientational dynamics in liquids[https://www.ch.ic.ac.uk/wiki/index.php/Talk:Mod:Hunt_Research_Group/legendre link]
#Functional for ILs using CPMD [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/IL_cpmd_functional link]
#Solving the angular part of the Schrödinger equation for a hydrogen atom [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/angular_schrodinger link] (notes by Vincent)

===Admin Stuff===
#Not used to writing a wiki, make your test runs [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/testing on this page]
#How to set-up new macs [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/mac_setup link]
#How to set-up remote desktop [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/mac_remote link]
#[https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/calendar Calendar]
#Demonstrating in the 3rd year computational chemistry lab [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/compchemlab Timetable]
#How to switch the printer HP CP3525dn duplex on and off [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/printing link]

Talk:Mod:Hunt Research Group/QMMM OPT Aqeuous Cu(II)

2013-09-10T10:37:09Z

Vhc08:

This ChemShell code runs a QM/MM geometry optimisation on our copper(II)-water system:

<pre>
newopt function = copt : { coords=cu_18water.pun
theory= hybrid : { coupling=shift
qm_region = {1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22}
qm_theory=gaussian : { basis=6-311g g98_mem=80000000 charge=2 mult=2 hamiltonian=b3lyp }
mm_theory=dl_poly : mm_defs=ff.dat
}
result=cu_18water_qmmm_opt.pun
}
</pre>

The <code>newopt</code> command invokes a general purpose optimiser code. The target function <code>copt</code> carries out the optimisation in Cartesian co-ordinates.

The initial co-ordinates are taken from [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/ChemShell_System_Aqeuous_Cu(II) here] while the force field parameters were defined [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/QMMM_SP_Aqeuous_Cu(II) here].

To run the optimisation, login to cx1 and submit the code via the PBS queue system. (Details [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/ChemShell_Introduction here])
If the optimisation is successful, you should see something like this at the end of the <code>.out</code> file:
<pre>
--------------------------------------------------------------------------------
********************************************************************************
Optimisation finished successfully
********************************************************************************
Results have been written to cu_18water_qmmm_opt.pun
newopt/copt/===================================== Tstep: 0.0 Ttot:42371.2 ==
newopt/copt/hybrid.kill/========================= Tstep: 0.0 Ttot:42371.2 ==
...hybrid.kill/dl_poly.kill/===================== Tstep: 0.0 Ttot:42371.2 ==

******************************* DL_POLY finished *******************************

MM termination code: 0
Energy and gradient evaluations:
QM energies 203
QM gradients 203
MM energies 203
MM gradients 203
no: end of optimisation
ChemShell exiting code 0
</pre>

The optimised structure is outputted into <code>cu_18water_qmmm_opt.pun</code>, which should look something like this:
<pre>
block = fragment records = 0
block = title records = 1
molecule 1
block = coordinates records = 55
cu -3.76257780766541e+00 6.39581622755847e+00 4.18666084467700e+00
o -8.61211193402496e-02 7.64015048162733e-01 9.28566236359741e-01
h 1.21543269728197e+00 1.88270779646951e+00 1.31175606629519e-01
h 6.37781706300753e-01 -7.82734221778962e-02 2.38728556418122e+00
o -4.51642283433391e+00 8.77759819691374e+00 1.46678151077030e+00
h -3.49172990884007e+00 1.03072164818830e+01 1.11089581484648e+00
h -5.54866802060477e+00 8.25158794461243e+00 -1.97852968619387e-02
o -4.95471761998812e+00 8.71052570690642e+00 6.83662498793940e+00
h -4.05605484296627e+00 1.01570572540756e+01 7.49895970199808e+00
h -6.87371317404838e+00 8.63461596505159e+00 6.95816954313609e+00
o -9.51480700603425e+00 7.65268168973318e+00 6.49527652838249e+00
h -1.08191880350448e+01 8.52142478395586e+00 5.45922246856226e+00
h -1.02602478290014e+01 6.29462819566987e+00 7.55178619381274e+00
o 1.21783543029695e-02 8.18965965674802e+00 4.64643593288696e+00
h 1.70179143020656e+00 7.88361340447555e+00 3.95575265334706e+00
h 1.53560458819001e-02 9.55384358956816e+00 5.90422029240048e+00
o -4.02073293122077e+00 3.61793980085322e+00 1.74997219960407e+00
h -2.59371465606442e+00 2.44468654734398e+00 1.36433254970553e+00
h -5.67098509457942e+00 3.09821229178831e+00 1.07603574755595e+00
o -3.38985817557272e+00 3.79310802899656e+00 6.74770649250538e+00
h -3.25082227534437e+00 4.17399732561277e+00 8.58047932923543e+00
h -3.61597049183051e+00 1.96919514808289e+00 6.37114616477612e+00
o 4.88512549227045e+00 7.32303960143179e+00 3.03802690857829e+00
h 5.90371157876586e+00 6.25868175713396e+00 4.23890965743296e+00
h 5.97736349003507e+00 8.77594531470776e+00 2.48511559337944e+00
o -4.29916411874004e+00 -2.37226641024922e+00 8.55602074665862e-01
h -4.48197927494656e+00 -4.02399646204200e+00 -6.12604734180689e-02
h -2.77416381761238e+00 -1.45943015368469e+00 1.60090770859538e-01
o -1.15152916911611e+01 3.91507445983514e+00 9.09487558613262e+00
h -1.31397292921642e+01 4.04276654045411e+00 1.00694432162367e+01
h -1.08607626672630e+01 2.15038777612147e+00 9.32363260523809e+00
o -7.26161532617709e-01 1.18925561409003e+01 8.16570819162541e+00
h -3.38210015169806e-02 1.17120023508492e+01 9.92714273176291e+00
h -6.83632570128503e-01 1.37379782847602e+01 7.71682993448162e+00
o -2.02526336260395e+00 1.27938834288615e+01 5.91933212826634e-02
h -2.59260481593547e+00 1.45962476869073e+01 2.42272907816360e-01
h -6.60720242454038e-01 1.27504221632937e+01 -1.26012417899430e+00
o -3.94420311392931e+00 -9.99442342009302e-01 5.75664862690226e+00
h -4.25433895488514e+00 -1.52750992694953e+00 3.94311845980275e+00
h -4.00360780860933e+00 -2.57522517852673e+00 6.81366036938644e+00
o -1.30415098084718e+01 9.80484470829646e+00 3.78198257557867e+00
h -1.48929394074433e+01 9.81272313216625e+00 4.20334863832536e+00
h -1.27734330674330e+01 1.10379592139561e+01 2.36612507894359e+00
o 3.18343925559676e+00 3.99162245471456e+00 -7.01690759967063e-01
h 4.03998156283156e+00 4.31487863453482e+00 -2.36245736355065e+00
h 3.80617991301159e+00 5.30361078391041e+00 5.32356523409876e-01
o -7.34841503128147e+00 7.18270192875724e+00 -2.19006910801384e+00
h -8.06775536858874e+00 5.50688446733079e+00 -1.63361378230881e+00
h -7.98466645635603e+00 7.54260798655164e+00 -3.94099354583780e+00
o -8.74477062425801e+00 2.67357572335193e+00 2.06916587181714e-01
h -9.21569433472465e+00 1.05523926189405e+00 -6.69813132357446e-01
h -1.01226940595264e+01 3.05868782112006e+00 1.45407977156667e+00
o -3.09052434169466e+00 4.63395423526394e+00 1.16058757972695e+01
h -4.36175688579645e+00 5.67645850057569e+00 1.25528664304173e+01
h -1.86140317121958e+00 3.92461378513185e+00 1.28658799243406e+01
block = connectivity records = 38
1 5
1 17
2 3
2 4
5 6
5 7
8 9
8 10
11 12
11 13
14 15
14 16
17 18
17 19
20 21
20 22
23 24
23 25
26 27
26 28
29 30
29 31
32 33
32 34
35 36
35 37
38 39
38 40
41 42
41 43
44 45
44 46
47 48
47 49
50 51
50 52
53 54
53 55
</pre>

Talk:Mod:Hunt Research Group/QMMM SP Aqeuous Cu(II)

2013-09-10T10:33:25Z

Vhc08:

== QM/MM Single Point Energy Calculation of Cu(II) and 2 Solvation Shells ==
In this example, the first solvation shell is modelled at the B3LYP 6-311G level (via Gaussian) while the second solvation shell is modelled using a classical pairwise potential (via DL_POLY).

Create an input file called <code>energy.chm</code> with the following content:
<pre>

energy energy=e coords=cu_18water.pun \
theory= hybrid : { coupling=shift
qm_region = {1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22}
qm_theory=gaussian : { basis=6-311g g98_mem=80000000 charge=2 mult=2 hamiltonian=b3lyp}
mm_theory=dl_poly : mm_defs=ff.dat
}
</pre>

The co-ordinates of the system are read from <code>cu_18water.pun</code> (created [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/ChemShell_System_Aqeuous_Cu(II) here]).
The first 22 atoms (Cu(II) + 7 waters in the first solvation shell) are modelled at the B3LYP 6-311G level.
The rest of the system is modelled using the force field defined in <code>ff.dat</code> (see [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/ChemShell_Force_Field_Parameters_Aqueous_Cu(II) here] for details).
The QM and MM regions are coupled via the charge shift scheme.

The calculation should be submitted to the PBS queue to avoid overloading the login shell and inconveniencing other cx1 users.
Make sure your submit script includes instructions to load Gaussian, DL_POLY and ChemShell.
Details can be found [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/ChemShell_Introduction here].

The energy can be found at the end of the output (<code>energy.out</code>):
<pre>
-----------------------------------------------------------------------------------
Energy ( hybrid): -2175.199009 (a.u.)
-----------------------------------------------------------------------------------
ChemShell exiting code 0
</pre>

Talk:Mod:Hunt Research Group/ChemShell Force Field Parameters Aqueous Cu(II)

2013-09-10T10:31:16Z

Vhc08:

== Creating a File Containing Force Field Parameters ==

The following ChemShell code generates a file called <code>ff.dat</code> which contains force field parameters for our copper-water system:
<pre>
read_input ff.dat {
vdw cu cu 62.99111 19858.39
vdw cu o 204.1966 118331.2
vdw cu h 0.000000 0.000000
vdw o o 626.00 630437.34
vdw o h 0.0000 0.000
vdw h h 0.0000 0.000
bond o h 1108.57 1.000
charge o -0.8476
charge h 0.4238
charge cu 2.0000
angle h o h 91.5392 109.4
}
</pre>
To run, login to cx1, put the code into a file (call it <code>ff.chm</code>). Make sure the ChemShell module is loaded (<code>module load chemshell/3.5.0</code>), and then execute:
<pre>
chemsh.x ff.chm
</pre>

If successful, you should see <code>ff.dat</code> created with the following contents:
<pre>
vdw cu cu 62.99111 19858.39
vdw cu o 204.1966 118331.2
vdw cu h 0.000000 0.000000
vdw o o 626.00 630437.34
vdw o h 0.0000 0.000
vdw h h 0.0000 0.000
bond o h 1108.57 1.000
charge o -0.8476
charge h 0.4238
charge cu 2.0000
angle h o h 91.5392 109.4
</pre>

<code>ff.dat</code> can be directly used as input into our copper-water ChemShell calculations which involve a force field.

The <code>vdw</code> keyword specifies pairwise non-bonded Lennard-Jones interactions.

The <code>bond</code> keyword specifies harmonic bond parameters between two atoms.

The <code>charge</code> keyword sets the electrostatic charge on an atom.

The <code>angle</code> keyword specifies harmonic angular terms between 3 atoms.

More details on these terms and other terms can be found [http://www.cse.scitech.ac.uk/ccg/software/chemshell/manual/dl_poly.html#SECTION00143000000000000000 here].

'''NB: Be careful when transferring parameters from a different program into ChemShell as they may be defined differently and/or have different units! See the table below for an example.
'''

{| class="wikitable"
! Program
! Keyword
! Potential Form
! Param. 1 (default units)
! Param. 2 (default units)
|-
|ChemShell
|<code>vdw</code>
|<math>U(r_{ij}) = -\frac{C_6}{r_{ij}^6} + \frac{C_{12}}{r_{ij}^{12}}</math>
|<math>C_6</math> (kcal mol<math>^{-1}</math> Å<math>^6</math>)
|<math>C_{12}</math> (kcal mol<math>^{-1}</math> Å<math>^{12}</math>)
|-
|DL_POLY
|<code>lj</code>
|<math>U(r_{ij}) = 4\epsilon\left[\left(\frac{\sigma}{r_{ij}}\right)^{12} - \left(\frac{\sigma}{r_{ij}}\right)^6\right]</math>
|<math>\epsilon</math> (J mol<math>^{-1}</math>)
|<math>\sigma</math> (Å)
|-
|}

Talk:Mod:Hunt Research Group/ChemShell Force Field Parameters Aqueous Cu(II)

2013-09-10T10:30:53Z

Vhc08:

== Creating a File Containing Force Field Parameters ==

The following ChemShell code generates a file called <code>ff.dat</code> which contains force field parameters for our copper-water system:
<pre>
read_input ff.dat {
vdw cu cu 62.99111 19858.39
vdw cu o 204.1966 118331.2
vdw cu h 0.000000 0.000000
vdw o o 626.00 630437.34
vdw o h 0.0000 0.000
vdw h h 0.0000 0.000
bond o h 1108.57 1.000
charge o -0.8476
charge h 0.4238
charge cu 2.0000
angle h o h 91.5392 109.4
}
</pre>
To run, login to cx1, put the code into a file (call it <code>ff.chm</code>). Make sure the ChemShell module is loaded (<code>module load chemshell/3.5.0</code>), and then execute:
<pre>
chemsh.x ff.chm
</pre>

If successful, you should see <code>ff.dat</code> created with the following contents:
<pre>
vdw cu cu 62.99111 19858.39
vdw cu o 204.1966 118331.2
vdw cu h 0.000000 0.000000
vdw o o 626.00 630437.34
vdw o h 0.0000 0.000
vdw h h 0.0000 0.000
bond o h 1108.57 1.000
charge o -0.8476
charge h 0.4238
charge cu 2.0000
angle h o h 91.5392 109.4
</pre>

<code>ff.dat</code> can be directly used as input into our copper-water ChemShell calculations which involve a force field.

The <code>vdw</code> keyword specifies pairwise non-bonded Lennard-Jones interactions.

The <code>bond</code> keyword specifies harmonic bond parameters between two atoms.

The <code>charge</code> keyword sets the electrostatic charge on an atom.

The <code>angle</code> keyword specifies harmonic angular terms between 3 atoms.

More details on these terms and other terms can be found [http://www.cse.scitech.ac.uk/ccg/software/chemshell/manual/dl_poly.html#SECTION00143000000000000000 here].

'''NB:Be careful when transferring parameters from a different program into ChemShell as they may be defined differently and/or have different units! See the table below for an example.
'''

{| class="wikitable"
! Program
! Keyword
! Potential Form
! Param. 1 (default units)
! Param. 2 (default units)
|-
|ChemShell
|<code>vdw</code>
|<math>U(r_{ij}) = -\frac{C_6}{r_{ij}^6} + \frac{C_{12}}{r_{ij}^{12}}</math>
|<math>C_6</math> (kcal mol<math>^{-1}</math> Å<math>^6</math>)
|<math>C_{12}</math> (kcal mol<math>^{-1}</math> Å<math>^{12}</math>)
|-
|DL_POLY
|<code>lj</code>
|<math>U(r_{ij}) = 4\epsilon\left[\left(\frac{\sigma}{r_{ij}}\right)^{12} - \left(\frac{\sigma}{r_{ij}}\right)^6\right]</math>
|<math>\epsilon</math> (J mol<math>^{-1}</math>)
|<math>\sigma</math> (Å)
|-
|}

Talk:Mod:Hunt Research Group/ChemShell Force Field Parameters Aqueous Cu(II)

2013-09-10T10:30:24Z

Vhc08:

== Creating a File Containing Force Field Parameters ==

The following ChemShell code generates a file called <code>ff.dat</code> which contains force field parameters for our copper-water system:
<pre>
read_input ff.dat {
vdw cu cu 62.99111 19858.39
vdw cu o 204.1966 118331.2
vdw cu h 0.000000 0.000000
vdw o o 626.00 630437.34
vdw o h 0.0000 0.000
vdw h h 0.0000 0.000
bond o h 1108.57 1.000
charge o -0.8476
charge h 0.4238
charge cu 2.0000
angle h o h 91.5392 109.4
}
</pre>
To run, put the code into a file (call it <code>ff.chm</code>), make sure the ChemShell module is loaded (<code>module load chemshell/3.5.0</code>), and then execute:
<pre>
chemsh.x ff.chm
</pre>

If successful, you should see <code>ff.dat</code> created with the following contents:
<pre>
vdw cu cu 62.99111 19858.39
vdw cu o 204.1966 118331.2
vdw cu h 0.000000 0.000000
vdw o o 626.00 630437.34
vdw o h 0.0000 0.000
vdw h h 0.0000 0.000
bond o h 1108.57 1.000
charge o -0.8476
charge h 0.4238
charge cu 2.0000
angle h o h 91.5392 109.4
</pre>

<code>ff.dat</code> can be directly used as input into our copper-water ChemShell calculations which involve a force field.

The <code>vdw</code> keyword specifies pairwise non-bonded Lennard-Jones interactions.

The <code>bond</code> keyword specifies harmonic bond parameters between two atoms.

The <code>charge</code> keyword sets the electrostatic charge on an atom.

The <code>angle</code> keyword specifies harmonic angular terms between 3 atoms.

More details on these terms and other terms can be found [http://www.cse.scitech.ac.uk/ccg/software/chemshell/manual/dl_poly.html#SECTION00143000000000000000 here].

'''NB:Be careful when transferring parameters from a different program into ChemShell as they may be defined differently and/or have different units! See the table below for an example.
'''

{| class="wikitable"
! Program
! Keyword
! Potential Form
! Param. 1 (default units)
! Param. 2 (default units)
|-
|ChemShell
|<code>vdw</code>
|<math>U(r_{ij}) = -\frac{C_6}{r_{ij}^6} + \frac{C_{12}}{r_{ij}^{12}}</math>
|<math>C_6</math> (kcal mol<math>^{-1}</math> Å<math>^6</math>)
|<math>C_{12}</math> (kcal mol<math>^{-1}</math> Å<math>^{12}</math>)
|-
|DL_POLY
|<code>lj</code>
|<math>U(r_{ij}) = 4\epsilon\left[\left(\frac{\sigma}{r_{ij}}\right)^{12} - \left(\frac{\sigma}{r_{ij}}\right)^6\right]</math>
|<math>\epsilon</math> (J mol<math>^{-1}</math>)
|<math>\sigma</math> (Å)
|-
|}

Talk:Mod:Hunt Research Group/ChemShell System Aqeuous Cu(II)

2013-09-10T10:14:05Z

Vhc08:

== Creating the Fragment Input ==

This fragment of copper(II) and its first 2 solvation shells (18 waters in total) was taken from a DL_POLY molecular dynamics trajectory of copper(II) and 200 waters.

The following ChemShell input generates a ChemShell readable input file (<code>cu_18water.pun</code>) from xyz coordinates in units of Angstroms:

<pre>
c_create coords=cu_18water.pun {

coordinates angstrom
cu -2.1208E+00 3.2333E+00 2.3434E+00
o -2.8625E-01 1.9061E+00 1.4529E+00
h 1.1877E-01 1.9593E+00 5.4012E-01
h -1.9888E-01 9.7326E-01 1.8024E+00
o -2.8223E+00 4.6610E+00 7.9753E-01
h -2.2564E+00 5.4307E+00 5.0188E-01
h -3.5063E+00 4.4613E+00 9.5864E-02
o -2.2571E+00 4.7205E+00 4.1738E+00
h -1.4037E+00 5.2415E+00 4.1604E+00
h -2.8973E+00 5.1460E+00 4.8133E+00
o -4.2411E+00 3.2562E+00 3.0943E+00
h -4.9570E+00 3.6912E+00 2.5482E+00
h -4.6604E+00 2.7121E+00 3.8210E+00
o -1.4300E-01 4.4480E+00 2.3166E+00
h 6.3987E-01 3.9559E+00 1.9358E+00
h 7.7886E-02 5.4206E+00 2.3892E+00
o -3.1399E+00 1.6922E+00 1.1368E+00
h -2.9742E+00 7.0608E-01 1.1396E+00
h -3.6503E+00 1.9421E+00 3.1389E-01
o -1.7364E+00 1.6708E+00 3.9303E+00
h -1.7041E+00 1.7025E+00 4.9292E+00
h -1.4097E+00 7.7998E-01 3.6143E+00
o 2.6020E+00 3.6347E+00 1.7248E+00
h 2.2869E+00 2.7841E+00 2.1456E+00
h 3.5362E+00 3.8286E+00 2.0243E+00
o -1.9034E+00 -7.5686E-01 4.9718E-01
h -2.0945E+00 -1.6870E+00 1.8370E-01
h -1.1600E+00 -3.6788E-01 -4.6901E-02
o -5.6797E+00 1.7355E+00 4.7967E+00
h -5.8293E+00 1.4817E+00 5.7523E+00
h -5.8000E+00 9.3087E-01 4.2153E+00
o -5.1385E-01 6.7028E+00 4.4103E+00
h 4.4713E-01 6.6035E+00 4.6685E+00
h -9.3334E-01 7.4261E+00 4.9588E+00
o -1.1217E+00 6.4841E+00 -2.9124E-01
h -3.5854E-01 7.0546E+00 1.2319E-02
h -9.3302E-01 6.1362E+00 -1.2096E+00
o -1.1420E+00 -8.1002E-01 3.1063E+00
h -1.7135E+00 -8.8594E-01 2.2893E+00
h -1.4996E+00 -1.4119E+00 3.8204E+00
o -6.3313E+00 4.8810E+00 1.7867E+00
h -6.4945E+00 5.6501E+00 2.4046E+00
h -6.7951E+00 5.0483E+00 9.1666E-01
o 1.3702E+00 2.5529E+00 -7.4590E-01
h 1.5559E+00 2.5872E+00 -1.7279E+00
h 2.2224E+00 2.6882E+00 -2.4052E-01
o -3.7986E+00 3.7196E+00 -1.4375E+00
h -4.4600E+00 3.0462E+00 -1.1074E+00
h -3.1624E+00 3.2791E+00 -2.0711E+00
o -5.4847E+00 1.8194E+00 -5.5093E-01
h -5.8739E+00 1.6589E+00 -1.4580E+00
h -6.1653E+00 1.5985E+00 1.4762E-01
o -2.3098E+00 2.6902E+00 6.4691E+00
h -2.9839E+00 3.4216E+00 6.5726E+00
h -1.7180E+00 2.6659E+00 7.2748E+00
}
</pre>
This simple script can be directly run on the cx1 login shell. First, make sure ChemShell loaded:

<pre>
module load chemshell/3.5.0
</pre>

Save the ChemShell code into a file (call it <code>cu_18water.chm</code>) and run it using the following command:
<pre>
chemsh.x cu_18water.chm
</pre>

If successful, you should see a file called <code>cu_18water.pun</code> in your working directory. The file should containing the following:
<pre>
block = fragment records = 0
block = title records = 1
molecule 1
block = coordinates records = 55
cu -4.00773230797269e+00 6.11005322112792e+00 4.42838546327008e+00
o -5.40934257429829e-01 3.60200799331702e+00 2.74558386941414e+00
h 2.24442835825121e-01 3.70254145181577e+00 1.02067916549519e+00
h -3.75828838838932e-01 1.83919537252805e+00 3.40604333831100e+00
o -5.33337556242517e+00 8.80801597862160e+00 1.50711370594938e+00
h -4.26397924354468e+00 1.02625385915255e+01 9.48416017882559e-01
h -6.62594860026623e+00 8.43063756391859e+00 1.81156756870753e-01
o -4.26530205220914e+00 8.92045471510046e+00 7.88734114815937e+00
h -2.65260931756944e+00 9.90500230678934e+00 7.86201881086833e+00
h -5.47510506218845e+00 9.72453341042410e+00 9.09582134947422e+00
o -8.01451975261362e+00 6.15332796172230e+00 5.84738121489998e+00
h -9.36737507102065e+00 6.97535906034929e+00 4.81540148395700e+00
h -8.80688214262349e+00 5.12512768410634e+00 7.22064558127293e+00
o -2.70230912881976e-01 8.40550419929390e+00 4.37774078868801e+00
h 1.20917940018035e+00 7.47556970818047e+00 3.65813287522328e+00
h 1.47183250914165e-01 1.02434523522240e+01 4.51493494445886e+00
o -5.93355275075605e+00 3.19779545999216e+00 2.14824127107853e+00
h -5.62042504261239e+00 1.33429820257137e+00 2.15353250573636e+00
h -6.89806923981172e+00 3.67003815320339e+00 5.93166302409254e-01
o -3.28132137851932e+00 3.15735530939304e+00 7.42719270559461e+00
h -3.22028320728794e+00 3.21725964462632e+00 9.31484066977507e+00
h -2.66394767755050e+00 1.47394900300478e+00 6.83003907992535e+00
o 4.91706877845385e+00 6.86858950386096e+00 3.25940054922260e+00
h 4.32161590678175e+00 5.26118800387908e+00 4.05459752922774e+00
h 6.68245142750519e+00 7.23500750391561e+00 3.82537368494394e+00
o -3.59690573132554e+00 -1.43025852254442e+00 9.39534302564061e-01
h -3.95803249672236e+00 -3.18796888134191e+00 3.47142788086846e-01
h -2.19208292967197e+00 -6.95192644972176e-01 -8.86300702452975e-02
o -1.07330805307396e+01 3.27962062452216e+00 9.06445188685995e+00
h -1.10157836396007e+01 2.80000799732324e+00 1.08702746865104e+01
h -1.09604146483599e+01 1.75908985926185e+00 7.96576480469505e+00
o -9.71036046044778e-01 1.26664598801770e+01 8.33426150407956e+00
h 8.44953483055369e-01 1.24788100224904e+01 8.82218892859793e+00
h -1.76375748412072e+00 1.40332991758940e+01 9.37077657901497e+00
o -2.11970639845953e+00 1.22531766588673e+01 -5.50363993480745e-01
h -6.77542597934990e-01 1.33312657203999e+01 2.32795427677836e-02
h -1.76315277158840e+00 1.15957407526320e+01 -2.28581337218208e+00
o -2.15806784972878e+00 -1.53071639197663e+00 5.87005793486211e+00
h -3.23804663792493e+00 -1.67418444027033e+00 4.32615125077417e+00
h -2.83383410460008e+00 -2.66810507621022e+00 7.21951174527482e+00
o -1.19644264246829e+01 9.22375584459387e+00 3.37637462969389e+00
h -1.22728298161678e+01 1.06771446214997e+01 4.54403673507691e+00
h -1.28408816512190e+01 9.53990711539915e+00 1.73223684337337e+00
o 2.58930347434184e+00 4.82428319927549e+00 -1.40954711831235e+00
h 2.94022571575571e+00 4.88910082383390e+00 -3.26525870187948e+00
h 4.19972853698533e+00 5.07996321684844e+00 -4.54517057107502e-01
o -7.17831570401030e+00 7.02902729759298e+00 -2.71648207879608e+00
h -8.42818091925602e+00 5.75648536238513e+00 -2.09268330717133e+00
h -5.97607160068503e+00 6.19660270231669e+00 -3.91381289279622e+00
o -1.03645838313550e+01 3.43816869159068e+00 -1.04110711072774e+00
h -1.11000654487933e+01 3.13486756209727e+00 -2.75522147539805e+00
h -1.16507317985402e+01 3.02072807162125e+00 2.78961450067393e-01
o -4.36489064737614e+00 5.08374267017546e+00 1.22248307589146e+01
h -5.63875539124844e+00 6.46588875186691e+00 1.24204174685879e+01
h -3.24655040791073e+00 5.03782231225216e+00 1.37473835317049e+01
block = connectivity records = 38
1 5
1 17
2 3
2 4
5 6
5 7
8 9
8 10
11 12
11 13
14 15
14 16
17 18
17 19
20 21
20 22
23 24
23 25
26 27
26 28
29 30
29 31
32 33
32 34
35 36
35 37
38 39
38 40
41 42
41 43
44 45
44 46
47 48
47 49
50 51
50 52
53 54
53 55
</pre>

This <code>.pun</code> file can serve as input to other ChemShell calculations.

Talk:Mod:Hunt Research Group/ChemShell System Aqeuous Cu(II)

2013-09-10T10:07:06Z

Vhc08:

Talk:Mod:Hunt Research Group/ChemShell System Aqeuous Cu(II)

2013-09-10T10:06:39Z

Vhc08:

== Creating the Fragment Input ==

This fragment of copper(II) and its first 2 solvation shells (18 waters in total) was taken from a DL_POLY molecular dynamics trajectory of copper(II) and 200 waters.

The following ChemShell input generates a ChemShell readable input file (<code>cu_18water.pun</code>) from xyz coordinates in units of Angstroms:

<pre>
c_create coords=cu_18water.pun {

coordinates angstrom
cu -2.1208E+00 3.2333E+00 2.3434E+00
o -2.8625E-01 1.9061E+00 1.4529E+00
h 1.1877E-01 1.9593E+00 5.4012E-01
h -1.9888E-01 9.7326E-01 1.8024E+00
o -2.8223E+00 4.6610E+00 7.9753E-01
h -2.2564E+00 5.4307E+00 5.0188E-01
h -3.5063E+00 4.4613E+00 9.5864E-02
o -2.2571E+00 4.7205E+00 4.1738E+00
h -1.4037E+00 5.2415E+00 4.1604E+00
h -2.8973E+00 5.1460E+00 4.8133E+00
o -4.2411E+00 3.2562E+00 3.0943E+00
h -4.9570E+00 3.6912E+00 2.5482E+00
h -4.6604E+00 2.7121E+00 3.8210E+00
o -1.4300E-01 4.4480E+00 2.3166E+00
h 6.3987E-01 3.9559E+00 1.9358E+00
h 7.7886E-02 5.4206E+00 2.3892E+00
o -3.1399E+00 1.6922E+00 1.1368E+00
h -2.9742E+00 7.0608E-01 1.1396E+00
h -3.6503E+00 1.9421E+00 3.1389E-01
o -1.7364E+00 1.6708E+00 3.9303E+00
h -1.7041E+00 1.7025E+00 4.9292E+00
h -1.4097E+00 7.7998E-01 3.6143E+00
o 2.6020E+00 3.6347E+00 1.7248E+00
h 2.2869E+00 2.7841E+00 2.1456E+00
h 3.5362E+00 3.8286E+00 2.0243E+00
o -1.9034E+00 -7.5686E-01 4.9718E-01
h -2.0945E+00 -1.6870E+00 1.8370E-01
h -1.1600E+00 -3.6788E-01 -4.6901E-02
o -5.6797E+00 1.7355E+00 4.7967E+00
h -5.8293E+00 1.4817E+00 5.7523E+00
h -5.8000E+00 9.3087E-01 4.2153E+00
o -5.1385E-01 6.7028E+00 4.4103E+00
h 4.4713E-01 6.6035E+00 4.6685E+00
h -9.3334E-01 7.4261E+00 4.9588E+00
o -1.1217E+00 6.4841E+00 -2.9124E-01
h -3.5854E-01 7.0546E+00 1.2319E-02
h -9.3302E-01 6.1362E+00 -1.2096E+00
o -1.1420E+00 -8.1002E-01 3.1063E+00
h -1.7135E+00 -8.8594E-01 2.2893E+00
h -1.4996E+00 -1.4119E+00 3.8204E+00
o -6.3313E+00 4.8810E+00 1.7867E+00
h -6.4945E+00 5.6501E+00 2.4046E+00
h -6.7951E+00 5.0483E+00 9.1666E-01
o 1.3702E+00 2.5529E+00 -7.4590E-01
h 1.5559E+00 2.5872E+00 -1.7279E+00
h 2.2224E+00 2.6882E+00 -2.4052E-01
o -3.7986E+00 3.7196E+00 -1.4375E+00
h -4.4600E+00 3.0462E+00 -1.1074E+00
h -3.1624E+00 3.2791E+00 -2.0711E+00
o -5.4847E+00 1.8194E+00 -5.5093E-01
h -5.8739E+00 1.6589E+00 -1.4580E+00
h -6.1653E+00 1.5985E+00 1.4762E-01
o -2.3098E+00 2.6902E+00 6.4691E+00
h -2.9839E+00 3.4216E+00 6.5726E+00
h -1.7180E+00 2.6659E+00 7.2748E+00
}
</pre>
This simple script can be directly run on the cx1 login shell. First, make sure ChemShell loaded:

<pre>
module load chemshell/3.5.0
</pre>

Save the ChemShell code into a file (call it <code>cu_18water.chm</code>) and run it using the following command:
<pre>
chemsh.x cu_18water.chm
</pre>

If successful, you should see a file called <code>cu_18water.pun</code> in your working directory. The file should containing the following:
<pre>
block = fragment records = 0
block = title records = 1
molecule 1
block = coordinates records = 55
cu -4.00773230797269e+00 6.11005322112792e+00 4.42838546327008e+00
o -5.40934257429829e-01 3.60200799331702e+00 2.74558386941414e+00
h 2.24442835825121e-01 3.70254145181577e+00 1.02067916549519e+00
h -3.75828838838932e-01 1.83919537252805e+00 3.40604333831100e+00
o -5.33337556242517e+00 8.80801597862160e+00 1.50711370594938e+00
h -4.26397924354468e+00 1.02625385915255e+01 9.48416017882559e-01
h -6.62594860026623e+00 8.43063756391859e+00 1.81156756870753e-01
o -4.26530205220914e+00 8.92045471510046e+00 7.88734114815937e+00
h -2.65260931756944e+00 9.90500230678934e+00 7.86201881086833e+00
h -5.47510506218845e+00 9.72453341042410e+00 9.09582134947422e+00
o -8.01451975261362e+00 6.15332796172230e+00 5.84738121489998e+00
h -9.36737507102065e+00 6.97535906034929e+00 4.81540148395700e+00
h -8.80688214262349e+00 5.12512768410634e+00 7.22064558127293e+00
o -2.70230912881976e-01 8.40550419929390e+00 4.37774078868801e+00
h 1.20917940018035e+00 7.47556970818047e+00 3.65813287522328e+00
h 1.47183250914165e-01 1.02434523522240e+01 4.51493494445886e+00
o -5.93355275075605e+00 3.19779545999216e+00 2.14824127107853e+00
h -5.62042504261239e+00 1.33429820257137e+00 2.15353250573636e+00
h -6.89806923981172e+00 3.67003815320339e+00 5.93166302409254e-01
o -3.28132137851932e+00 3.15735530939304e+00 7.42719270559461e+00
h -3.22028320728794e+00 3.21725964462632e+00 9.31484066977507e+00
h -2.66394767755050e+00 1.47394900300478e+00 6.83003907992535e+00
o 4.91706877845385e+00 6.86858950386096e+00 3.25940054922260e+00
h 4.32161590678175e+00 5.26118800387908e+00 4.05459752922774e+00
h 6.68245142750519e+00 7.23500750391561e+00 3.82537368494394e+00
o -3.59690573132554e+00 -1.43025852254442e+00 9.39534302564061e-01
h -3.95803249672236e+00 -3.18796888134191e+00 3.47142788086846e-01
h -2.19208292967197e+00 -6.95192644972176e-01 -8.86300702452975e-02
o -1.07330805307396e+01 3.27962062452216e+00 9.06445188685995e+00
h -1.10157836396007e+01 2.80000799732324e+00 1.08702746865104e+01
h -1.09604146483599e+01 1.75908985926185e+00 7.96576480469505e+00
o -9.71036046044778e-01 1.26664598801770e+01 8.33426150407956e+00
h 8.44953483055369e-01 1.24788100224904e+01 8.82218892859793e+00
h -1.76375748412072e+00 1.40332991758940e+01 9.37077657901497e+00
o -2.11970639845953e+00 1.22531766588673e+01 -5.50363993480745e-01
h -6.77542597934990e-01 1.33312657203999e+01 2.32795427677836e-02
h -1.76315277158840e+00 1.15957407526320e+01 -2.28581337218208e+00
o -2.15806784972878e+00 -1.53071639197663e+00 5.87005793486211e+00
h -3.23804663792493e+00 -1.67418444027033e+00 4.32615125077417e+00
h -2.83383410460008e+00 -2.66810507621022e+00 7.21951174527482e+00
o -1.19644264246829e+01 9.22375584459387e+00 3.37637462969389e+00
h -1.22728298161678e+01 1.06771446214997e+01 4.54403673507691e+00
h -1.28408816512190e+01 9.53990711539915e+00 1.73223684337337e+00
o 2.58930347434184e+00 4.82428319927549e+00 -1.40954711831235e+00
h 2.94022571575571e+00 4.88910082383390e+00 -3.26525870187948e+00
h 4.19972853698533e+00 5.07996321684844e+00 -4.54517057107502e-01
o -7.17831570401030e+00 7.02902729759298e+00 -2.71648207879608e+00
h -8.42818091925602e+00 5.75648536238513e+00 -2.09268330717133e+00
h -5.97607160068503e+00 6.19660270231669e+00 -3.91381289279622e+00
o -1.03645838313550e+01 3.43816869159068e+00 -1.04110711072774e+00
h -1.11000654487933e+01 3.13486756209727e+00 -2.75522147539805e+00
h -1.16507317985402e+01 3.02072807162125e+00 2.78961450067393e-01
o -4.36489064737614e+00 5.08374267017546e+00 1.22248307589146e+01
h -5.63875539124844e+00 6.46588875186691e+00 1.24204174685879e+01
h -3.24655040791073e+00 5.03782231225216e+00 1.37473835317049e+01
block = connectivity records = 38
1 5
1 17
2 3
2 4
5 6
5 7
8 9
8 10
11 12
11 13
14 15
14 16
17 18
17 19
20 21
20 22
23 24
23 25
26 27
26 28
29 30
29 31
32 33
32 34
35 36
35 37
38 39
38 40
41 42
41 43
44 45
44 46
47 48
47 49
50 51
50 52
53 54
53 55
</pre>

This <code>.pun</code> input file can then serve as input to other ChemShell calculations.

Talk:Mod:Hunt Research Group/ChemShell Introduction

2013-09-10T10:01:29Z

Vhc08:

This tutorial will outline the basics of ChemShell leading to a QM/MM calculation of copper(II) and 2 solvation shells.

ChemShell inputs are written in Tcl (Tool Command Language) can be run either interactively or as a script on cx1.

To run ChemShell commands on the login shell, you will need to first load the ChemShell module at the login shell after logging in to cx1:
<pre>
module load chemshell/3.5.0
</pre>
The interactive mode is then invoked by entering <code>chemsh.x</code>.
Alternatively, you can run scripts via the command:
<pre>
chemsh.x NAME_OF_SCRIPT
</pre>
where <code>NAME_OF_SCRIPT</code> is the name of script containing the ChemShell commands you want to run.

==Submitting via the Portable Batch System (PBS)==
To ensure that you are not hogging computing resources on the login shell and inconveniencing other cx1 users, it is best to run your calculations (except the most basic calculations/actions) by submitting to the Portable Batch System (PBS).

A typical submit script will look like the following:

<pre>
#/bin/sh
#PBS -l walltime=48:00:00
#PBS -l mem=2600MB
#PBS -j oe

module load dl_poly/2.19 intel-suite mpi
module load gaussian/g09
module load chemshell/3.5.0

cp $PBS_O_WORKDIR/energy.chm $TMPDIR
cp $PBS_O_WORKDIR/ff.dat $TMPDIR
cp $PBS_O_WORKDIR/cu_18water.pun $TMPDIR

cd $TMPDIR
mpiexec chemsh.x energy.chm > energy.out

cp $TMPDIR/* $PBS_O_WORKDIR/
</pre>

The command <code>module load</code> loads modules required for the calculation.
In this example submit script for a QM/MM calculation, DL_POLY (for MM), Gaussian (for QM) as well as ChemShell are required.

The following <code>cp</code> commands copies all the input files into the temporary directory (<code>$TMPDIR</code>) for running the calculation.

The command <code>mpiexec chemsh.x energy.chm > energy.out</code> instructs ChemShell to execute the script called <code>energy.chm</code> and to write any standard output into <code>energy.out</code>.

The final <code>cp</code> command copies all output files (includes <code>energy.out</code> along with others) back into your working directory at the end.

To submit a script like this into the PBS queue, enter the following at the command line:
<pre>
qsub NAME_OF_SCRIPT
</pre>
where <code>NAME_OF_SCRIPT</code> is the name of the script.

Talk:Mod:Hunt Research Group/ChemShell Introduction

2013-09-10T10:01:05Z

Vhc08:

This tutorial will outline the basics of ChemShell leading to a QM/MM calculation of copper(II) and 2 solvation shells.

ChemShell inputs are written in Tcl (Tool Command Language) can be run either interactively or as a script on cx1.

To run ChemShell commands on the login shell, you will need to first load the ChemShell module at the login shell after logging in to cx1:
<pre>
module load chemshell/3.5.0
</pre>
The interactive mode is then invoked by entering <code>chemsh.x</code>.
Alternatively, you can run scripts via the command:
<pre>
chemsh.x NAME_OF_SCRIPT
</pre>
where <code>NAME_OF_SCRIPT</code> is the name of script containing the ChemShell commands you want to run.

==Submitting via the Portable Batch System (PBS)==
To ensure that you are not hogging computing resources on the login shell and inconveniencing other cx1 users, it is best to run your calculations (except the most basic calculations/actions) by submitting to the Portable Batch System (PBS).

A typical submit script will look like the following:

<pre>
#/bin/sh
#PBS -l walltime=48:00:00
#PBS -l mem=2600MB
#PBS -j oe

module load dl_poly/2.19 intel-suite mpi
module load gaussian/g09
module load chemshell/3.5.0

cp $PBS_O_WORKDIR/energy.chm $TMPDIR
cp $PBS_O_WORKDIR/ff.dat $TMPDIR
cp $PBS_O_WORKDIR/cu_18water.pun $TMPDIR

cd $TMPDIR
mpiexec chemsh.x energy.chm > energy.out

cp $TMPDIR/* $PBS_O_WORKDIR/
</pre>

The command <code>module load</code> loads modules required for the calculation.
In this example submit script for a QM/MM calculation, DL_POLY (for MM), Gaussian (for QM) as well as ChemShell are required.

The following <code>cp</code> commands copies all the input files into the temporary directory (<code>$TMPDIR</code>) for running the calculation.

The command <code>mpiexec chemsh.x energy.chm > energy.out</code> instructs ChemShell to execute the script called <code>energy.chm</code> and to write any standard output into <code>energy.out</code>

The final <code>cp</code> command copies all output files (includes <code>energy.out</code> along with others) back into your working directory at the end.

To submit a script like this into the PBS queue, enter the following at the command line:
<pre>
qsub NAME_OF_SCRIPT
</pre>
where <code>NAME_OF_SCRIPT</code> is the name of the script.

Talk:Mod:Hunt Research Group/ChemShell Introduction

2013-09-10T09:58:59Z

Vhc08:

This tutorial will outline the basics of ChemShell leading to a QM/MM calculation of copper(II) and 2 solvation shells.

ChemShell inputs are written in Tcl (Tool Command Language) can be run either interactively or as a script on cx1.

To run ChemShell commands on the login shell, you will need to first load the ChemShell module at the login shell after logging in to cx1:
<pre>
module load chemshell/3.5.0
</pre>
The interactive mode is then invoked by entering <code>chemsh.x</code>.
Alternatively, you can run scripts via the command:
<pre>
chemsh.x NAME_OF_SCRIPT
</pre>
where <code>NAME_OF_SCRIPT</code> is the name of script containing the ChemShell commands you want to run.

==Submitting via the Portable Batch System (PBS)==
To ensure that you are not hogging computing resources on the login shell and inconveniencing other cx1 users, it is best to run your calculations (except the most basic calculations/actions) by submitting to the Portable Batch System (PBS).

A typical submit script will look like the following:

<pre>
#/bin/sh
#PBS -l walltime=48:00:00
#PBS -l mem=2600MB
#PBS -j oe

module load dl_poly/2.19 intel-suite mpi
module load gaussian/g09
module load chemshell/3.5.0

cp $PBS_O_WORKDIR/energy.chm $TMPDIR
cp $PBS_O_WORKDIR/ff.dat $TMPDIR
cp $PBS_O_WORKDIR/cu_18water.pun $TMPDIR

cd $TMPDIR
mpiexec chemsh.x energy.chm > energy.out

cp $TMPDIR/* $PBS_O_WORKDIR/
</pre>

The command <code>module load</code> is used to load all the modules required for the calculation.
In this example submit script for a QM/MM calculation, DL_POLY (for MM), Gaussian (for QM) as well as ChemShell are required.

In addition, the <code>cp</code> command is used to copy all the input files into the temporary directory (<code>$TMPDIR</code>) for running the calculation.

The command <code>mpiexec chemsh.x energy.chm > energy.out</code> instructs ChemShell to execute the script called <code>energy.chm</code> and to write any standard output into <code>energy.out</code>

The final command copies all output files (includes <code>energy.out</code> along with others) back into your working directory at the end.

To submit a script like this into the queue, enter the following at the command line:
<pre>
qsub NAME_OF_SCRIPT
</pre>
where <code>NAME_OF_SCRIPT</code> is the name of the script.

Talk:Mod:Hunt Research Group/ChemShell Introduction

2013-09-10T09:58:34Z

Vhc08:

This tutorial will outline the basics of ChemShell leading to a QM/MM calculation of copper(II) and 2 solvation shells.

ChemShell inputs are written in Tcl (Tool Command Language) can be run either interactively or as a script on cx1.

To run ChemShell commands on the login shell, you will need to first load the ChemShell module at the login shell after logging in to cx1:
<pre>
module load chemshell/3.5.0
</pre>
The interactive mode is then invoked by entering <code>chemsh.x</code>.
Alternatively, you can run scripts via the command:
<pre>
chemsh.x NAME_OF_SCRIPT
</pre>
where <code>NAME_OF_SCRIPT</code> is the name of script containing the ChemShell commands you want to run.

==Submitting via the Portable Batch System (PBS)==
However, to ensure that you are not hogging computing resources on the login shell and inconveniencing other cx1 users, it is best to run your calculations (except perhaps the most basic calculations/actions) by submitting to the Portable Batch System (PBS).

A typical submit script will look like the following:

<pre>
#/bin/sh
#PBS -l walltime=48:00:00
#PBS -l mem=2600MB
#PBS -j oe

module load dl_poly/2.19 intel-suite mpi
module load gaussian/g09
module load chemshell/3.5.0

cp $PBS_O_WORKDIR/energy.chm $TMPDIR
cp $PBS_O_WORKDIR/ff.dat $TMPDIR
cp $PBS_O_WORKDIR/cu_18water.pun $TMPDIR

cd $TMPDIR
mpiexec chemsh.x energy.chm > energy.out

cp $TMPDIR/* $PBS_O_WORKDIR/
</pre>

The command <code>module load</code> is used to load all the modules required for the calculation.
In this example submit script for a QM/MM calculation, DL_POLY (for MM), Gaussian (for QM) as well as ChemShell are required.

In addition, the <code>cp</code> command is used to copy all the input files into the temporary directory (<code>$TMPDIR</code>) for running the calculation.

The command <code>mpiexec chemsh.x energy.chm > energy.out</code> instructs ChemShell to execute the script called <code>energy.chm</code> and to write any standard output into <code>energy.out</code>

The final command copies all output files (includes <code>energy.out</code> along with others) back into your working directory at the end.

To submit a script like this into the queue, enter the following at the command line:
<pre>
qsub NAME_OF_SCRIPT
</pre>
where <code>NAME_OF_SCRIPT</code> is the name of the script.

Talk:Mod:Hunt Research Group/ChemShell Introduction

2013-09-10T09:58:03Z

Vhc08:

This tutorial will outline the basics of ChemShell leading to a QM/MM calculation of copper(II) and 2 solvation shells.

ChemShell inputs are written in Tcl (Tool Command Language) can be run either interactively or as a script on cx1.

To run ChemShell commands on the login shell, you will need to first load the ChemShell module at the login shell after logging in to cx1:
<pre>
module load chemshell/3.5.0
</pre>
The interactive mode is then invoked by entering <code>chemsh.x</code>.
Alternatively, you can run scripts via the command:
<pre>
chemsh.x NAME_OF_SCRIPT
</pre>
where <code>NAME_OF_SCRIPT</code> is the name of script containing the ChemShell commands you want to run.

However, to ensure that you are not hogging computing resources on the login shell and inconveniencing other cx1 users, it is best to run your calculations (except perhaps the most basic calculations/actions) by submitting to the Portable Batch System (PBS).

A typical submit script will look like the following:

<pre>
#/bin/sh
#PBS -l walltime=48:00:00
#PBS -l mem=2600MB
#PBS -j oe

module load dl_poly/2.19 intel-suite mpi
module load gaussian/g09
module load chemshell/3.5.0

cp $PBS_O_WORKDIR/energy.chm $TMPDIR
cp $PBS_O_WORKDIR/ff.dat $TMPDIR
cp $PBS_O_WORKDIR/cu_18water.pun $TMPDIR

cd $TMPDIR
mpiexec chemsh.x energy.chm > energy.out

cp $TMPDIR/* $PBS_O_WORKDIR/
</pre>

The command <code>module load</code> is used to load all the modules required for the calculation.
In this example submit script for a QM/MM calculation, DL_POLY (for MM), Gaussian (for QM) as well as ChemShell are required.

In addition, the <code>cp</code> command is used to copy all the input files into the temporary directory (<code>$TMPDIR</code>) for running the calculation.

The command <code>mpiexec chemsh.x energy.chm > energy.out</code> instructs ChemShell to execute the script called <code>energy.chm</code> and to write any standard output into <code>energy.out</code>

The final command copies all output files (includes <code>energy.out</code> along with others) back into your working directory at the end.

To submit a script like this into the queue, enter the following at the command line:
<pre>
qsub NAME_OF_SCRIPT
</pre>
where <code>NAME_OF_SCRIPT</code> is the name of the script.

Talk:Mod:Hunt Research Group/ChemShell Introduction

2013-09-10T09:57:26Z

Vhc08:

This tutorial will outline the basics of ChemShell leading to a QM/MM calculation of copper(II) and 2 solvation shells.

ChemShell inputs are written in Tcl (Tool Command Language) can be run either interactively or as a script on cx1.

To run ChemShell commands on the login shell, you will need to first load the ChemShell module at the login shell after logging in to cx1:
<pre>
module load chemshell/3.5.0
</pre>
The interactive mode is then invoked by entering <code>chemsh.x</code>.
Alternatively, you can run scripts via the command:
<pre>
chemsh.x NAME_OF_SCRIPT
</pre>
where <code>NAME_OF_SCRIPT</code> is the name of script.

However, to ensure that you are not hogging computing resources on the login shell and inconveniencing other cx1 users, it is best to run your calculations (except perhaps the most basic calculations/actions) by submitting to the Portable Batch System (PBS).

A typical submit script will look like the following:

<pre>
#/bin/sh
#PBS -l walltime=48:00:00
#PBS -l mem=2600MB
#PBS -j oe

module load dl_poly/2.19 intel-suite mpi
module load gaussian/g09
module load chemshell/3.5.0

cp $PBS_O_WORKDIR/energy.chm $TMPDIR
cp $PBS_O_WORKDIR/ff.dat $TMPDIR
cp $PBS_O_WORKDIR/cu_18water.pun $TMPDIR

cd $TMPDIR
mpiexec chemsh.x energy.chm > energy.out

cp $TMPDIR/* $PBS_O_WORKDIR/
</pre>

The command <code>module load</code> is used to load all the modules required for the calculation.
In this example submit script for a QM/MM calculation, DL_POLY (for MM), Gaussian (for QM) as well as ChemShell are required.

In addition, the <code>cp</code> command is used to copy all the input files into the temporary directory (<code>$TMPDIR</code>) for running the calculation.

The command <code>mpiexec chemsh.x energy.chm > energy.out</code> instructs ChemShell to execute the script called <code>energy.chm</code> and to write any standard output into <code>energy.out</code>

The final command copies all output files (includes <code>energy.out</code> along with others) back into your working directory at the end.

To submit a script like this into the queue, enter the following at the command line:
<pre>
qsub NAME_OF_SCRIPT
</pre>
where <code>NAME_OF_SCRIPT</code> is the name of the script containing the ChemShell commands you would like to run.

Talk:Mod:Hunt Research Group/ChemShell Introduction

2013-09-10T09:05:51Z

Vhc08:

This tutorial will outline the basics of ChemShell leading to a QM/MM calculation of copper(II) and 2 solvation shells.

ChemShell inputs are written in Tcl (Tool Command Language) can be run either interactively or as a script on cx1.

To run ChemShell commands interactively, you will need to load the ChemShell module at the login shell after logging in to cx1:
<pre>
module load chemshell/3.5.0
</pre>

However, to ensure that you are not hogging computing resources on the login shell and inconveniencing other cx1 users, it is best to run your calculations (except perhaps the most basic calculations/actions) by submitting to the Portable Batch System (PBS).

A typical submit script will look like the following:

<pre>
#/bin/sh
#PBS -l walltime=48:00:00
#PBS -l mem=2600MB
#PBS -j oe

module load dl_poly/2.19 intel-suite mpi
module load gaussian/g09
module load chemshell/3.5.0

cp $PBS_O_WORKDIR/energy.chm $TMPDIR
cp $PBS_O_WORKDIR/ff.dat $TMPDIR
cp $PBS_O_WORKDIR/cu_18water.pun $TMPDIR

cd $TMPDIR
mpiexec chemsh.x energy.chm > energy.out

cp $TMPDIR/* $PBS_O_WORKDIR/
</pre>

The command <code>module load</code> is used to load all the modules required for the calculation.
In this example submit script for a QM/MM calculation, DL_POLY (for MM), Gaussian (for QM) as well as ChemShell are required.

In addition, the <code>cp</code> command is used to copy all the input files into the temporary directory (<code>$TMPDIR</code>) for running the calculation.

The command <code>mpiexec chemsh.x energy.chm > energy.out</code> instructs ChemShell to execute the script called <code>energy.chm</code> and to write any standard output into <code>energy.out</code>

The final command copies all output files (includes <code>energy.out</code> along with others) back into your working directory at the end.

To submit a script like this into the queue, enter the following at the command line:
<pre>
qsub NAME_OF_SCRIPT
</pre>
where <code>NAME_OF_SCRIPT</code> is the name of the script.

Talk:Mod:Hunt Research Group/ChemShell Introduction

2013-09-10T09:02:17Z

Vhc08:

This tutorial will outline the basics of ChemShell leading to a QM/MM calculation of copper(II) and 2 solvation shells.

In order you run ChemShell, you will have to login to cx1 and load the ChemShell module via the following command:

<pre>
module load chemshell/3.5.0
</pre>

ChemShell inputs are written in Tcl (Tool Command Language) can be run either interactively or as a script.
To ensure that you are not hogging computing power on the login shell and inconveniencing other cx1 users, it is best to run your calculations (except perhaps the most basic calculations/actions) via the <code>qsub</code> submit system.

A typical submit script will look like the following:

<pre>
#/bin/sh
#PBS -l walltime=48:00:00
#PBS -l mem=2600MB
#PBS -j oe

module load dl_poly/2.19 intel-suite mpi
module load gaussian/g09
module load chemshell/3.5.0

cp $PBS_O_WORKDIR/energy.chm $TMPDIR
cp $PBS_O_WORKDIR/ff.dat $TMPDIR
cp $PBS_O_WORKDIR/cu_18water.pun $TMPDIR

cd $TMPDIR
mpiexec chemsh.x energy.chm > energy.out

cp $TMPDIR/* $PBS_O_WORKDIR/
</pre>

The command <code>module load</code> is used to load all the modules required for the calculation.
In this example submit script for a QM/MM calculation, DL_POLY (for MM), Gaussian (for QM) as well as ChemShell are required.

In addition, the <code>cp</code> command is used to copy all the input files into the temporary directory (<code>$TMPDIR</code>) for running the calculation.

The command <code>mpiexec chemsh.x energy.chm > energy.out</code> instructs ChemShell to execute the script called <code>energy.chm</code> and to write any standard output into <code>energy.out</code>

The final command copies all output files (includes <code>energy.out</code> along with others) back into your working directory at the end.

To submit a script like this into the queue, enter the following at the command line:
<pre>
qsub NAME_OF_SCRIPT
</pre>
where <code>NAME_OF_SCRIPT</code> is the name of the script.