ChemWiki - User contributions [en]

Rep:Title=Mod:CJS test

2016-02-15T16:11:18Z

Cjs14:

==My Test Page==

<pre>

Item Value Threshold Converged?
Maximum Force 0.000323 0.000450 YES
RMS Force 0.000153 0.000300 YES
Maximum Displacement 0.001116 0.001800 YES
RMS Displacement 0.000922 0.001200 YES

</pre>

DOI Link[http://doi.org/10042/a3v2u]

Some test writing

<ref name="ja9825332">W. T. Klooster , T. F. Koetzle , P. E. M. Siegbahn , T. B. Richardson , and R. H. Crabtree, "Study of the N-H···H-B Dihydrogen Bond Including the Crystal Structure of BH3NH3 by Neutron Diffraction", ''J. Am. Chem. Soc.'', '''1999''', ''121'', 6337–6343.{{DOI|10.1021/ja9825332}}</ref>

<math>a+b=c^2</math>

some more text<ref name="ja9825332" />

<jmolFile text="A link to an uploaded .mol file">my_test_mol.mol</jmolFile>

<jmol>
<jmolApplet>
<title>Pentahelicene</title><color>white</color>
<size>150</size><script>zoom 5;moveto 4 0 2 0 90 120;spin 2;</script>
<uploadedFileContents>my_test_mol.mol</uploadedFileContents>
</jmolApplet>
</jmol>


<jmol>
<jmolApplet>
<title>Vibration</title><color>white</color><size>200</size>
<script>frame 8;vectors 4;vectors scale 5.0;color vectors red;vibration 10;
</script><uploadedFileContents>BCl3-09.log</uploadedFileContents>
</jmolApplet>
</jmol>

<jmol>
<jmolApplet>
<title>Orbital</title><color>white</color><size>300</size>
<script>isosurface color orange purple "images/1/1b/AHB_mo22-2.cub.jvxl" translucent;</script>
<uploadedFileContents>AHB_mo22.xyz</uploadedFileContents>
</jmolApplet>
</jmol>

Rep:Title=Mod:CJS test

2016-02-15T12:19:06Z

Cjs14: /* My Test Page */

==My Test Page==

<pre>

Item Value Threshold Converged?
Maximum Force 0.000323 0.000450 YES
RMS Force 0.000153 0.000300 YES
Maximum Displacement 0.001116 0.001800 YES
RMS Displacement 0.000922 0.001200 YES

</pre>

(DOI Link)[http://doi.org/10042/a3v2u]

Some test writing

<ref name="ja9825332">W. T. Klooster , T. F. Koetzle , P. E. M. Siegbahn , T. B. Richardson , and R. H. Crabtree, "Study of the N-H···H-B Dihydrogen Bond Including the Crystal Structure of BH3NH3 by Neutron Diffraction", ''J. Am. Chem. Soc.'', '''1999''', ''121'', 6337–6343.{{DOI|10.1021/ja9825332}}</ref>

<math>a+b=c^2</math>

some more text<ref name="ja9825332" />

<jmolFile text="A link to an uploaded .mol file">my_test_mol.mol</jmolFile>

<jmol>
<jmolApplet>
<title>Pentahelicene</title><color>white</color>
<size>150</size><script>zoom 5;moveto 4 0 2 0 90 120;spin 2;</script>
<uploadedFileContents>my_test_mol.mol</uploadedFileContents>
</jmolApplet>
</jmol>


<jmol>
<jmolApplet>
<title>Vibration</title><color>white</color><size>200</size>
<script>frame 8;vectors 4;vectors scale 5.0;color vectors red;vibration 10;
</script><uploadedFileContents>BCl3-09.log</uploadedFileContents>
</jmolApplet>
</jmol>

<jmol>
<jmolApplet>
<title>Orbital</title><color>white</color><size>300</size>
<script>isosurface color orange purple "images/1/1b/AHB_mo22-2.cub.jvxl" translucent;</script>
<uploadedFileContents>AHB_mo22.xyz</uploadedFileContents>
</jmolApplet>
</jmol>

Rep:Title=Mod:CJS test

2016-02-15T12:17:34Z

Cjs14: Created page with "==My Test Page== (DOI Link)[http://doi.org/10042/a3v2u] Some test writing <ref name="ja9825332">W. T. Klooster , T. F. Koetzle , P. E. M. Siegbahn , T. B. Richardson , and..."

==My Test Page==

(DOI Link)[http://doi.org/10042/a3v2u]

Some test writing

<ref name="ja9825332">W. T. Klooster , T. F. Koetzle , P. E. M. Siegbahn , T. B. Richardson , and R. H. Crabtree, "Study of the N-H···H-B Dihydrogen Bond Including the Crystal Structure of BH3NH3 by Neutron Diffraction", ''J. Am. Chem. Soc.'', '''1999''', ''121'', 6337–6343.{{DOI|10.1021/ja9825332}}</ref>

<math>a+b=c^2</math>

some more text<ref name="ja9825332" />

<jmolFile text="A link to an uploaded .mol file">my_test_mol.mol</jmolFile>

<jmol>
<jmolApplet>
<title>Pentahelicene</title><color>white</color>
<size>150</size><script>zoom 5;moveto 4 0 2 0 90 120;spin 2;</script>
<uploadedFileContents>my_test_mol.mol</uploadedFileContents>
</jmolApplet>
</jmol>


<jmol>
<jmolApplet>
<title>Vibration</title><color>white</color><size>200</size>
<script>frame 8;vectors 4;vectors scale 5.0;color vectors red;vibration 10;
</script><uploadedFileContents>BCl3-09.log</uploadedFileContents>
</jmolApplet>
</jmol>

<jmol>
<jmolApplet>
<title>Orbital</title><color>white</color><size>300</size>
<script>isosurface color orange purple "images/1/1b/AHB_mo22-2.cub.jvxl" translucent;</script>
<uploadedFileContents>AHB_mo22.xyz</uploadedFileContents>
</jmolApplet>
</jmol>

User:Cjs14

2016-02-15T12:11:34Z

Cjs14: /* My Test Page */

User:Cjs14

2016-02-15T12:10:08Z

Cjs14:

User:Cjs14

2016-02-15T12:08:43Z

Cjs14:

==My Test Page==

(DOI Link)[http://doi.org/10042/a3v2u]

Some test writing

<ref name="ja9825332">W. T. Klooster , T. F. Koetzle , P. E. M. Siegbahn , T. B. Richardson , and R. H. Crabtree, "Study of the N-H···H-B Dihydrogen Bond Including the Crystal Structure of BH3NH3 by Neutron Diffraction", ''J. Am. Chem. Soc.'', '''1999''', ''121'', 6337–6343.{{DOI|10.1021/ja9825332}}</ref>

<math>a+b=c^2</math>

some more text<ref name="ja9825332" />

<jmolFile text="A link to an uploaded .mol file">my_test_mol.mol</jmolFile>

<jmol>
<jmolApplet>
<title>Pentahelicene</title><color>white</color>
<size>150</size><script>zoom 5;moveto 4 0 2 0 90 120;spin 2;</script>
<uploadedFileContents>yourmolecule.cml</uploadedFileContents>
</jmolApplet>
</jmol>


<jmol>
<jmolApplet>
<title>Vibration</title><color>white</color><size>200</size>
<script>frame 8;vectors 4;vectors scale 5.0;color vectors red;vibration 10;
</script><uploadedFileContents>BCl3-09.log</uploadedFileContents>
</jmolApplet>
</jmol>

User:Cjs14

2016-02-15T12:03:01Z

Cjs14: /* My Test Page */

File:My test mol.mol

2016-02-15T12:01:58Z

Cjs14:

User:Cjs14

2016-02-15T11:49:47Z

Cjs14:

User:Cjs14

2016-02-15T11:48:53Z

Cjs14:

User:Cjs14

2016-02-15T11:45:58Z

Cjs14:

==My Test Page==

(DOI Link)[http://doi.org/10042/a3v2u]

Some test writing

<ref>abc</ref>

<math>a+b=c^2</math>

User:Cjs14

2016-02-15T11:44:58Z

Cjs14:

==My Test Page==

(DOI Link)[http://doi.org/10042/a3v2u]

Some test writing

<ref>abc</ref>

User:Cjs14

2016-02-15T11:44:28Z

Cjs14:

<head>
<title>MathJax TeX Test Page</title>
<script type="text/x-mathjax-config">
MathJax.Hub.Config({tex2jax: {inlineMath: [['$','$'], ['\$','\$']]}});
</script>
<script type="text/javascript" async
src="https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS_CHTML">
</script>
</head>

==My Test Page==

(DOI Link)[http://doi.org/10042/a3v2u]

Some test writing

<ref>abc</ref>

$$abc$$

User:Cjs14

2016-02-15T11:43:50Z

Cjs14:

<!DOCTYPE html>
<html>
<head>
<title>MathJax TeX Test Page</title>
<script type="text/x-mathjax-config">
MathJax.Hub.Config({tex2jax: {inlineMath: [['$','$'], ['\$','\$']]}});
</script>
<script type="text/javascript" async
src="https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS_CHTML">
</script>
</head>
<body>
When $a \ne 0$, there are two solutions to $ax^2 + bx + c = 0$ and they are
$$x = {-b \pm \sqrt{b^2-4ac} \over 2a}.$$
</body>
</html>

==My Test Page==

(DOI Link)[http://doi.org/10042/a3v2u]

Some test writing

<ref>abc</ref>

$$abc$$

User:Cjs14

2016-02-15T11:43:12Z

Cjs14: /* My Test Page */

User:Cjs14

2016-02-15T11:42:46Z

Cjs14:

==My Test Page==

(DOI Link)[http://doi.org/10042/a3v2u]

Some test writing

<ref>abc</ref>

<script type="text/x-mathjax-config">
MathJax.Hub.Config({tex2jax: {inlineMath: [['$','$'], ['\$','\$']]}});
</script>
<script type="text/javascript" async
src="https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS_CHTML">
</script>

$$abc$$

User:Cjs14

2016-02-15T11:39:30Z

Cjs14:

==My Test Page==

(DOI Link)[http://doi.org/10042/a3v2u]

Some test writing

<ref>abc</ref>

User:Cjs14

2016-02-15T11:37:38Z

Cjs14:

==My Test Page==

(DOI Link)[http://doi.org/10042/a3v2u]

Some test writing

$a=b$

User:Cjs14

2016-02-15T11:36:06Z

Cjs14:

==My Test Page==

(DOI Link)[http://doi.org/10042/a3v2u]

User:Cjs14

2016-02-15T11:35:21Z

Cjs14:

test
======

(DOI Link)[http://doi.org/10042/a3v2u]

User:Cjs14

2016-02-15T11:35:06Z

Cjs14:

test
====

(DOI Link)[http://doi.org/10042/a3v2u]

User:Cjs14

2016-02-15T11:34:41Z

Cjs14:

test
-----
(link)[http://doi.org/10042/a3v2u]

User:Cjs14

2016-02-15T11:34:08Z

Cjs14:

test
-----

<nowiki>-----</nowiki>

<nowiki>http://doi.org/10042/a3v2u</nowiki>

User:Cjs14

2016-02-15T11:33:48Z

Cjs14:

test

<nowiki>-----</nowiki>

<nowiki>http://doi.org/10042/a3v2u</nowiki>

User:Cjs14

2016-02-15T11:31:06Z

Cjs14: Created page with "test"

test

Mod:Hunt Research Group/calendar

2015-06-26T10:31:54Z

Cjs14:

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 (Done)
| Precious Ugbomah (Not Done)
|-
| Vincent Chen (Done)
| Gabriel Lau (Done)
| Rebecca Rowe (Not Done)
| Ken Watson (Done)
|-
| Aiswarya Prabha (Not Done)
| Richard Fogarty (Not Done)
| Christopher Sewell (Done)
| Chen Chen (Not Done)
|-
|Ziyun Zhang (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="#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 Bryan Away </td>
<td bgcolor="#cccccc">20th Bryan Away Gabriel Away (Boulder Conference) </td>
<td bgcolor="#cccccc">21st Bryan Away Gabriel Away (Boulder Conference) </td>
</tr>
<tr valign="top">
<td>22nd Bryan Away Gabriel Away (Boulder Conference) </td>
<td>23rd Bryan Away Gabriel Away (Boulder Conference) </td>
<td>24th Bryan Away Gabriel Away (Boulder Conference) </td>
<td>25th Bryan Away Richard F Exp Gabriel Away (Boulder Conference) </td>
<td>26th Bryan Away Gabriel Away (Boulder Conference) </td>
<td bgcolor="#cccccc">27th Bryan Away Gabriel Away </td>
<td bgcolor="#cccccc">28th Bryan Away Gabriel Away </td>
</tr>
<tr valign="top">
<td >29th Bryan Away Gabriel Away Chris Away </td>
<td>30th Chris Away </td>
<td bgcolor="#4357CFF">'''1st July''' Gabriel Away Chris Away </td>
<td>2nd Gabriel Away Chris Away </td>
<td>3rd Tricia Away Gabriel Away Chris Away </td>
<td bgcolor="#cccccc">4th Tricia Away Gabriel Away </td>
<td bgcolor="#cccccc">5th Tricia Away Gabriel Away </td>
</tr>
<tr valign="top">
<td >6th Tricia Away Gabriel Away </td>
<td>7th Richard F Exp Gabriel Away </td>
<td>8th Richard F Exp Gabriel Away Ken Away </td>
<td>9th Richard F Exp Gabriel Away Ken Away </td>
<td>10th Richard F Exp Gabriel Away Ken Away </td>
<td bgcolor="#cccccc">11th Gabriel Away (FOMMS Conference) </td>
<td bgcolor="#cccccc">12th Gabriel Away (FOMMS Conference) </td>
</tr>
<tr valign="top">
<td>13th Richard F Away Gabriel Away (FOMMS Conference) Chris Away </td>
<td>14th Gabriel Away (FOMMS Conference) Chris Away </td>
<td>15th Gabriel Away (FOMMS Conference) Chris Away </td>
<td>16th Gabriel Away (FOMMS Conference) Chris Away </td>
<td>17th Gabriel Away (FOMMS Conference) Chris Away </td>
<td bgcolor="#cccccc">18th </td>
<td bgcolor="#cccccc">19th </td>
</tr>
<tr valign="top">
<td>20th </td>
<td>21st Claire Away Chris Away </td>
<td>22nd Claire Away</td>
<td>23rd Claire Away</td>
<td>24th Claire Away</td>
<td bgcolor="#cccccc">25th Claire Away</td>
<td bgcolor="#cccccc">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="#cccccc">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="#cccccc">8th Tricia Away </td>
<td bgcolor="#cccccc">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="#cccccc">15th Tricia Away </td>
<td bgcolor="#cccccc">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="#cccccc">22nd </td>
<td bgcolor="#cccccc">23rd </td>
</tr>
<tr valign="top">
<td>24th </td>
<td>25th </td>
<td>26th </td>
<td>27th </td>
<td>28th </td>
<td bgcolor="#cccccc">29th </td>
<td bgcolor="#cccccc">30th </td>
</tr>
<tr valign="top">
<td bgcolor="#33CC99">31st '''Bank Holiday'''</td>
<td bgcolor="#4357CFF">'''1st September''' </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 </td>
<td>9th </td>
<td>10th </td>
<td>11th </td>
<td bgcolor="#cccccc">12th Tricia Away </td>
<td bgcolor="#cccccc">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="#cccccc">19th Tricia Away </td>
<td bgcolor="#cccccc">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="#cccccc">26th </td>
<td bgcolor="#cccccc">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="#ffff66">3rd '''TERM BEGINS'''</td>
<td bgcolor="#cccccc">4th </td>
</tr>
</table>

Mod:Hunt Research Group

2015-06-17T11:16:58Z

Cjs14: added link to documentation

==Hunt Group Wiki==

Back to the main [http://www.ch.ic.ac.uk/hunt web-page]
===HPC 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]
#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 make qsub more comfortable (gfunc) [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/pimpQSUB 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]

===Visualisation===
*'''density based visualisation'''
#download [http://aim.tkgristmill.com AIMALL]

*'''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: a molecular dynamics visualisation package'''
#Download VMD [//wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/download_vmd link]
#Quick reminder [https://www.ch.ic.ac.uk/wiki/index.php/Talk:Mod:Hunt_Research_Group/VMDReminder link]
#Tricks and tips [https://www.ch.ic.ac.uk/wiki/index.php/Talk:Mod:Hunt_Research_Group/VMDTips link]
#Changing the graphical representation of your structures [https://www.ch.ic.ac.uk/wiki/index.php/Talk:Mod:Hunt_Research_Group/vmd link]
#Basic visualisation of a trajectory [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]
#Using scripts in VMD [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/VmdScripts link]
#Dealing with periodic boundaries and bonding (under construction) [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/VmdScriptsPeriodic link]
#Dealing with bonding (under construction) [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/VmdBonding link]
#Atom selection and more advanced GUI based visualisation (under construction) [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/VmdVisual 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]
*'''PyGauss'''
#Python API for analysis of Gaussian compuations [https://pygauss.readthedocs.org - Documentation]

===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]
#M0n and DFT-D [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/DFTD link]
#IL ONIOM clusters [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/oniomclusers link]
#Molecular volume calculations [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group/molecular_volume link]
#problems with scf convergence [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/scf_convergence link]

===Setup and Running Ab-Initio MD Simulations===
#CPMD: Car-Parrinello Molecular Dynamics [https://www.ch.ic.ac.uk/wiki/index.php/Talk:Mod:Hunt_Research_Group/cpmd link]
#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===
#DLPOLY a MD simulation package, Installation on an IMac (old needs to be updated) [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/dlpoly_install link]
#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 started: generating a solvated structure and "relaxing" it [https://www.ch.ic.ac.uk/wiki/index.php/Talk:Mod:Hunt_Research_Group/Starting_MD link]
#local [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/packmol_to_dlpoly_scripts packmol to dlpoly] conversion scripts
#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]
#Energy Drift [https://www.ch.ic.ac.uk/wiki/index.php/Talk:Mod:Hunt_Research_Group/EnergyDrift 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]
#Using MolCluster [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/MolCluster 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)
#Systematic conformational scan for ion-pair dimers [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/ion_pair_scan link]

===Installing and using other packages===
#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/]

===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]
#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

2015-05-14T15:03:34Z

Cjs14: added link to my pygauss package

==Hunt Group Wiki==

Back to the main [http://www.ch.ic.ac.uk/hunt web-page]
===HPC 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]
#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 make qsub more comfortable (gfunc) [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/pimpQSUB 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]

===Visualisation===
*'''density based visualisation'''
#download [http://aim.tkgristmill.com AIMALL]

*'''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: a molecular dynamics visualisation package'''
#Download VMD [//wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/download_vmd link]
#Quick reminder [https://www.ch.ic.ac.uk/wiki/index.php/Talk:Mod:Hunt_Research_Group/VMDReminder link]
#Tricks and tips [https://www.ch.ic.ac.uk/wiki/index.php/Talk:Mod:Hunt_Research_Group/VMDTips link]
#Changing the graphical representation of your structures [https://www.ch.ic.ac.uk/wiki/index.php/Talk:Mod:Hunt_Research_Group/vmd link]
#Basic visualisation of a trajectory [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]
#Using scripts in VMD [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/VmdScripts link]
#Dealing with periodic boundaries and bonding (under construction) [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/VmdScriptsPeriodic link]
#Dealing with bonding (under construction) [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/VmdBonding link]
#Atom selection and more advanced GUI based visualisation (under construction) [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/VmdVisual 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]
*'''PyGauss'''
#Python API for analysis of Gaussian compuations [https://github.com/chrisjsewell/PyGauss/wiki 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]
#M0n and DFT-D [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/DFTD link]
#IL ONIOM clusters [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/oniomclusers link]
#Molecular volume calculations [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group/molecular_volume link]
#problems with scf convergence [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/scf_convergence link]

===Setup and Running Ab-Initio MD Simulations===
#CPMD: Car-Parrinello Molecular Dynamics [https://www.ch.ic.ac.uk/wiki/index.php/Talk:Mod:Hunt_Research_Group/cpmd link]
#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===
#DLPOLY a MD simulation package, Installation on an IMac (old needs to be updated) [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/dlpoly_install link]
#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 started: generating a solvated structure and "relaxing" it [https://www.ch.ic.ac.uk/wiki/index.php/Talk:Mod:Hunt_Research_Group/Starting_MD link]
#local [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/packmol_to_dlpoly_scripts packmol to dlpoly] conversion scripts
#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]
#Energy Drift [https://www.ch.ic.ac.uk/wiki/index.php/Talk:Mod:Hunt_Research_Group/EnergyDrift 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]
#Using MolCluster [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/MolCluster 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)
#Systematic conformational scan for ion-pair dimers [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/ion_pair_scan link]

===Installing and using other packages===
#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/]

===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]
#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/calendar

2015-03-31T15:50:30Z

Cjs14: /* Calendar */

Mod:Hunt Research Group/calendar

2015-03-31T15:50:04Z

Cjs14: /* Calendar */

Mod:Hunt Research Group/calendar

2015-03-31T15:49:24Z

Cjs14: /* Calendar */