ChemWiki - User contributions [en]

Talk:Mod:Hunt Research Group/Wheretostart

2014-08-06T16:59:26Z

Jt413:

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

==Introduction==
Before any MD simulations can be run we require a suitable MM force field (potential function).
For Ionic Liquids there are several MM force fields available. In our work we currently use
the Imidazolium based IL FF of Can-Lopes et al.

==Specific example using [EMIM]+[AlCl4]-==
*For this example, we refer to these two articles for force field parameters<ref>J. D. Andrade, E. S. Boes, H. Stassen, J. Phys. Chem. B, 2002, 106, 3546-3548</ref><ref>T. Fox, P. A. Kollman, J. Phys. Chem. B, 1998, 102, 8070-8079</ref>.
*In the reported articles, the AMBER force field functional form for the potential energy V is used:
[[File:WikiLJ.png|thumb|center|400px]]
*ε is the well depth and a measure of how strongly the two particles attract each other.
*σ is the distance at which the intermolecular potential between the two particles is zero.
*σ also gives a measure of how close two nonbonding particles can get and is thus referred to as the Van der Waals radius. It is equal to one-half of the internuclear distance between nonbonding particles.
*And lastly, r is the distance of separation between both particles (measured from the center of one particle to the center of the other particle).

*Start with 3 input files: CONFIG, CONTROL and FIELD
*CONFIG gives your initial configuration (obtained from packmol and converted), CONTROL gives your parameters, and FIELD provides the force field
*Sample input file FIELD:
<pre>
EMIM-ALCl4 - JPCB 2002 v.106 p.3546
units kJ
molecules 2
EMIM
nummols 128
atoms 19
CR 12.011000000 -0.11000 1
NA 14.006740000 0.15000 1
CW 12.011000000 -0.13000 1
CW 12.011000000 -0.13000 1
NA 14.006740000 0.15000 1
HCR 1.007940000 0.21000 1
HCW 1.007940000 0.21000 1
HCW 1.007940000 0.21000 1
C1 12.011000000 -0.17000 1
H1 1.007940000 0.13000 1
H1 1.007940000 0.13000 1
H1 1.007940000 0.13000 1
C1 12.011000000 -0.17000 1
H1 1.007940000 0.13000 1
H1 1.007940000 0.13000 1
C2 12.011000000 -0.05000 1
HC 1.007940000 0.06000 1
HC 1.007940000 0.06000 1
HC 1.007940000 0.06000 1
bonds 8
harm 1 2 3992.00000 1.3150
harm 1 5 3992.00000 1.3150
harm 2 3 3574.00000 1.3780
harm 5 4 3574.00000 1.3780
harm 2 9 2820.00000 1.4660
harm 5 13 2820.00000 1.4660
harm 3 4 4352.00000 1.3410
harm 13 16 2242.00000 1.5290
constrains 11
1 6 1.080000
4 8 1.080000
:
:
:
</pre>
*Explanation of above snapshot:
[[File:Wiki1.png|thumb|center|1100px]]

*scrolling down...
<pre>
:
:
:
angles 33
harm 5 1 2 585.20 109.8000
harm 6 1 2 292.60 125.1000
harm 6 1 5 292.60 125.1000
harm 1 2 3 585.20 108.0000
harm 1 5 4 585.20 108.0000
harm 2 3 7 292.60 122.0000
harm 5 4 8 292.60 122.0000
harm 2 3 4 585.20 107.1000
harm 5 4 3 585.20 107.1000
harm 8 4 3 292.60 130.9000
:
:
:
</pre>
*Explanation of above snapshot:
[[File:Wiki2.png|thumb|center|800px]]

*scrolling down more...
<pre>
:
:
:
dihedrals 46
cos3 6 1 2 9 0.000000 19.460000 0.000000 0.500000 0.500000
cos3 6 1 5 13 0.000000 19.460000 0.000000 0.500000 0.500000
cos3 6 1 2 3 0.000000 19.460000 0.000000 0.500000 0.500000
cos3 6 1 5 4 0.000000 19.460000 0.000000 0.500000 0.500000
cos3 1 2 3 7 0.000000 12.550000 0.000000 0.500000 0.500000
cos3 1 5 4 8 0.000000 12.550000 0.000000 0.500000 0.500000
:
:
:
</pre>
*Explanation of above snapshot:
Harmonic Dihedral Potential Vn/2 (1 + cos[nφ − γ]) from forcefield functional

*scrolling down even more...
<pre>
:
:
:
cos3 5 3 4 8 0.000000 9.200000 0.000000 0.500000 0.500000
cos3 2 4 3 7 0.000000 9.200000 0.000000 0.500000 0.500000
finish
alumcl
nummols 128
atoms 5
AL 26.9815400000 0.90920 1
CL 35.4530000000 -0.47730 4
bonds 4
harm 1 2 485.34000 2.1700
harm 1 3 485.34000 2.1700
harm 1 4 485.34000 2.1700
harm 1 5 485.34000 2.1700
angles 6
harm 3 1 2 209.20 109.5000
harm 4 1 2 209.20 109.5000
harm 5 1 2 209.20 109.5000
harm 4 1 3 209.20 109.5000
harm 5 1 3 209.20 109.5000
harm 5 1 4 209.20 109.5000
finish
vdW 66
CR CR lj 0.29288000 3.55000000
CR NA lj 0.45642051 3.39669000
CR CW lj 0.29288000 3.55000000
CR HCR lj 0.19173497 2.93104100
CR HCW lj 0.19173497 2.93104100
:
:
:
</pre>
*Explanation of above snapshot:
[[File:Wikiff4.png|thumb|center|900px]]
*Link to excel file with calculations for Lennard-Jones component [[Media:LJ-parameters.xlsx]]
*Link to PDF for the input file FIELD [[Media:FIELD.pdf]]

==Notes==
<references/>

==References==
*[1] http://pubs.acs.org/doi/full/10.1021/jp014229s
*[2] http://pubs.acs.org/doi/abs/10.1021/jp9717655

Talk:Mod:Hunt Research Group/Wheretostart

2014-08-06T16:59:12Z

Jt413:

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

==Introduction==
Before any MD simulations can be run we require a suitable MM force field (potential function).
For Ionic Liquids there are several MM force fields available. In our work we currently use
the Imidazolium based IL FF of Can-Lopes et al.

==Specific example using [EMIM]+[AlCl4]-==
*For this example, we refer to these two articles for force field parameters<ref>J. D. Andrade, E. S. Boes, H. Stassen, J. Phys. Chem. B, 2002, 106, 3546-3548</ref><ref>T. Fox, P. A. Kollman, J. Phys. Chem. B, 1998, 102, 8070-8079</ref>.
*In the reported articles, the AMBER force field functional form for the potential energy V is used:
[[File:WikiLJ.png|thumb|center|400px]]
*ε is the well depth and a measure of how strongly the two particles attract each other.
*σ is the distance at which the intermolecular potential between the two particles is zero.
*σ also gives a measure of how close two nonbonding particles can get and is thus referred to as the Van der Waals radius. It is equal to one-half of the internuclear distance between nonbonding particles.
*And lastly, r is the distance of separation between both particles (measured from the center of one particle to the center of the other particle).

*Start with 3 input files: CONFIG, CONTROL and FIELD
*CONFIG gives your initial configuration (obtained from packmol and converted), CONTROL gives your parameters, and FIELD provides the force field
*Sample input file FIELD:
<pre>
EMIM-ALCl4 - JPCB 2002 v.106 p.3546
units kJ
molecules 2
EMIM
nummols 128
atoms 19
CR 12.011000000 -0.11000 1
NA 14.006740000 0.15000 1
CW 12.011000000 -0.13000 1
CW 12.011000000 -0.13000 1
NA 14.006740000 0.15000 1
HCR 1.007940000 0.21000 1
HCW 1.007940000 0.21000 1
HCW 1.007940000 0.21000 1
C1 12.011000000 -0.17000 1
H1 1.007940000 0.13000 1
H1 1.007940000 0.13000 1
H1 1.007940000 0.13000 1
C1 12.011000000 -0.17000 1
H1 1.007940000 0.13000 1
H1 1.007940000 0.13000 1
C2 12.011000000 -0.05000 1
HC 1.007940000 0.06000 1
HC 1.007940000 0.06000 1
HC 1.007940000 0.06000 1
bonds 8
harm 1 2 3992.00000 1.3150
harm 1 5 3992.00000 1.3150
harm 2 3 3574.00000 1.3780
harm 5 4 3574.00000 1.3780
harm 2 9 2820.00000 1.4660
harm 5 13 2820.00000 1.4660
harm 3 4 4352.00000 1.3410
harm 13 16 2242.00000 1.5290
constrains 11
1 6 1.080000
4 8 1.080000
:
:
:
</pre>
*Explanation of above snapshot:
[[File:Wiki1.png|thumb|center|1100px]]

*scrolling down...
<pre>
:
:
:
angles 33
harm 5 1 2 585.20 109.8000
harm 6 1 2 292.60 125.1000
harm 6 1 5 292.60 125.1000
harm 1 2 3 585.20 108.0000
harm 1 5 4 585.20 108.0000
harm 2 3 7 292.60 122.0000
harm 5 4 8 292.60 122.0000
harm 2 3 4 585.20 107.1000
harm 5 4 3 585.20 107.1000
harm 8 4 3 292.60 130.9000
:
:
:
</pre>
*Explanation of above snapshot:
[[File:Wiki2.png|thumb|center|800px]]

*scrolling down more...
<pre>
:
:
:
dihedrals 46
cos3 6 1 2 9 0.000000 19.460000 0.000000 0.500000 0.500000
cos3 6 1 5 13 0.000000 19.460000 0.000000 0.500000 0.500000
cos3 6 1 2 3 0.000000 19.460000 0.000000 0.500000 0.500000
cos3 6 1 5 4 0.000000 19.460000 0.000000 0.500000 0.500000
cos3 1 2 3 7 0.000000 12.550000 0.000000 0.500000 0.500000
cos3 1 5 4 8 0.000000 12.550000 0.000000 0.500000 0.500000
:
:
:
</pre>
*Explanation of above snapshot:
Harmonic Dihedral Potential Vn/2 (1 + cos[nφ − γ]) from forcefield functional

*scrolling down even more...
<pre>
:
:
:
cos3 5 3 4 8 0.000000 9.200000 0.000000 0.500000 0.500000
cos3 2 4 3 7 0.000000 9.200000 0.000000 0.500000 0.500000
finish
alumcl
nummols 128
atoms 5
AL 26.9815400000 0.90920 1
CL 35.4530000000 -0.47730 4
bonds 4
harm 1 2 485.34000 2.1700
harm 1 3 485.34000 2.1700
harm 1 4 485.34000 2.1700
harm 1 5 485.34000 2.1700
angles 6
harm 3 1 2 209.20 109.5000
harm 4 1 2 209.20 109.5000
harm 5 1 2 209.20 109.5000
harm 4 1 3 209.20 109.5000
harm 5 1 3 209.20 109.5000
harm 5 1 4 209.20 109.5000
finish
vdW 66
CR CR lj 0.29288000 3.55000000
CR NA lj 0.45642051 3.39669000
CR CW lj 0.29288000 3.55000000
CR HCR lj 0.19173497 2.93104100
CR HCW lj 0.19173497 2.93104100
:
:
:
</pre>
*Explanation of above snapshot:
[[File:Wikiff4.png|thumb|center|900px]]
*Link to excel file with calculations for Lennard-Jones component [[Media:LJ-parameters.xlsx]]
*Link to PDF for the whole input file FIELD [[Media:FIELD.pdf]]

==Notes==
<references/>

==References==
*[1] http://pubs.acs.org/doi/full/10.1021/jp014229s
*[2] http://pubs.acs.org/doi/abs/10.1021/jp9717655

Talk:Mod:Hunt Research Group/Wheretostart

2014-08-06T16:53:28Z

Jt413:

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

==Introduction==
Before any MD simulations can be run we require a suitable MM force field (potential function).
For Ionic Liquids there are several MM force fields available. In our work we currently use
the Imidazolium based IL FF of Can-Lopes et al.

==Specific example using [EMIM]+[AlCl4]-==
*For this example, we refer to these two articles for force field parameters<ref>J. D. Andrade, E. S. Boes, H. Stassen, J. Phys. Chem. B, 2002, 106, 3546-3548</ref><ref>T. Fox, P. A. Kollman, J. Phys. Chem. B, 1998, 102, 8070-8079</ref>.
*In the reported articles, the AMBER force field functional form for the potential energy V is used:
[[File:WikiLJ.png|thumb|center|400px]]
*ε is the well depth and a measure of how strongly the two particles attract each other.
*σ is the distance at which the intermolecular potential between the two particles is zero.
*σ also gives a measure of how close two nonbonding particles can get and is thus referred to as the Van der Waals radius. It is equal to one-half of the internuclear distance between nonbonding particles.
*And lastly, r is the distance of separation between both particles (measured from the center of one particle to the center of the other particle).

*Start with 3 input files: CONFIG, CONTROL and FIELD
*CONFIG gives your initial configuration (obtained from packmol and converted), CONTROL gives your parameters, and FIELD provides the force field
*Sample input file FIELD:
<pre>
EMIM-ALCl4 - JPCB 2002 v.106 p.3546
units kJ
molecules 2
EMIM
nummols 128
atoms 19
CR 12.011000000 -0.11000 1
NA 14.006740000 0.15000 1
CW 12.011000000 -0.13000 1
CW 12.011000000 -0.13000 1
NA 14.006740000 0.15000 1
HCR 1.007940000 0.21000 1
HCW 1.007940000 0.21000 1
HCW 1.007940000 0.21000 1
C1 12.011000000 -0.17000 1
H1 1.007940000 0.13000 1
H1 1.007940000 0.13000 1
H1 1.007940000 0.13000 1
C1 12.011000000 -0.17000 1
H1 1.007940000 0.13000 1
H1 1.007940000 0.13000 1
C2 12.011000000 -0.05000 1
HC 1.007940000 0.06000 1
HC 1.007940000 0.06000 1
HC 1.007940000 0.06000 1
bonds 8
harm 1 2 3992.00000 1.3150
harm 1 5 3992.00000 1.3150
harm 2 3 3574.00000 1.3780
harm 5 4 3574.00000 1.3780
harm 2 9 2820.00000 1.4660
harm 5 13 2820.00000 1.4660
harm 3 4 4352.00000 1.3410
harm 13 16 2242.00000 1.5290
constrains 11
1 6 1.080000
4 8 1.080000
:
:
:
</pre>
*Explanation of above snapshot:
[[File:Wiki1.png|thumb|center|1100px]]

*scrolling down...
<pre>
:
:
:
angles 33
harm 5 1 2 585.20 109.8000
harm 6 1 2 292.60 125.1000
harm 6 1 5 292.60 125.1000
harm 1 2 3 585.20 108.0000
harm 1 5 4 585.20 108.0000
harm 2 3 7 292.60 122.0000
harm 5 4 8 292.60 122.0000
harm 2 3 4 585.20 107.1000
harm 5 4 3 585.20 107.1000
harm 8 4 3 292.60 130.9000
:
:
:
</pre>
*Explanation of above snapshot:
[[File:Wiki2.png|thumb|center|800px]]

*scrolling down more...
<pre>
:
:
:
dihedrals 46
cos3 6 1 2 9 0.000000 19.460000 0.000000 0.500000 0.500000
cos3 6 1 5 13 0.000000 19.460000 0.000000 0.500000 0.500000
cos3 6 1 2 3 0.000000 19.460000 0.000000 0.500000 0.500000
cos3 6 1 5 4 0.000000 19.460000 0.000000 0.500000 0.500000
cos3 1 2 3 7 0.000000 12.550000 0.000000 0.500000 0.500000
cos3 1 5 4 8 0.000000 12.550000 0.000000 0.500000 0.500000
:
:
:
</pre>
*Explanation of above snapshot:
Harmonic Dihedral Potential Vn/2 (1 + cos[nφ − γ]) from forcefield functional

*scrolling down even more...
<pre>
:
:
:
cos3 5 3 4 8 0.000000 9.200000 0.000000 0.500000 0.500000
cos3 2 4 3 7 0.000000 9.200000 0.000000 0.500000 0.500000
finish
alumcl
nummols 128
atoms 5
AL 26.9815400000 0.90920 1
CL 35.4530000000 -0.47730 4
bonds 4
harm 1 2 485.34000 2.1700
harm 1 3 485.34000 2.1700
harm 1 4 485.34000 2.1700
harm 1 5 485.34000 2.1700
angles 6
harm 3 1 2 209.20 109.5000
harm 4 1 2 209.20 109.5000
harm 5 1 2 209.20 109.5000
harm 4 1 3 209.20 109.5000
harm 5 1 3 209.20 109.5000
harm 5 1 4 209.20 109.5000
finish
vdW 66
CR CR lj 0.29288000 3.55000000
CR NA lj 0.45642051 3.39669000
CR CW lj 0.29288000 3.55000000
CR HCR lj 0.19173497 2.93104100
CR HCW lj 0.19173497 2.93104100
:
:
:
</pre>
*Explanation of above snapshot:
[[File:Wikiff4.png|thumb|center|900px]]
*Link to excel file with calculations for Lennard-Jones component [[Media:LJ-parameters.xlsx]]
*Link to PDF file for the whole input file FIELD [[Media:FIELD.pdf]]

==Notes==
<references/>

==References==
*[1] http://pubs.acs.org/doi/full/10.1021/jp014229s
*[2] http://pubs.acs.org/doi/abs/10.1021/jp9717655

Talk:Mod:Hunt Research Group/Wheretostart

2014-08-06T16:52:05Z

Jt413:

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

==Introduction==
Before any MD simulations can be run we require a suitable MM force field (potential function).
For Ionic Liquids there are several MM force fields available. In our work we currently use
the Imidazolium based IL FF of Can-Lopes et al.

==Specific example using [EMIM]+[AlCl4]-==
*For this example, we refer to these two articles for force field parameters<ref>J. D. Andrade, E. S. Boes, H. Stassen, J. Phys. Chem. B, 2002, 106, 3546-3548</ref><ref>T. Fox, P. A. Kollman, J. Phys. Chem. B, 1998, 102, 8070-8079</ref>.
*In the reported articles, the AMBER force field functional form for the potential energy V is used:
[[File:WikiLJ.png|thumb|center|400px]]
*ε is the well depth and a measure of how strongly the two particles attract each other.
*σ is the distance at which the intermolecular potential between the two particles is zero.
*σ also gives a measure of how close two nonbonding particles can get and is thus referred to as the Van der Waals radius. It is equal to one-half of the internuclear distance between nonbonding particles.
*And lastly, r is the distance of separation between both particles (measured from the center of one particle to the center of the other particle).

== ==
*Start with 3 input files: CONFIG, CONTROL and FIELD
*CONFIG gives your initial configuration (obtained from packmol and converted), CONTROL gives your parameters, and FIELD provides the force field
*Sample input file FIELD:
<pre>
EMIM-ALCl4 - JPCB 2002 v.106 p.3546
units kJ
molecules 2
EMIM
nummols 128
atoms 19
CR 12.011000000 -0.11000 1
NA 14.006740000 0.15000 1
CW 12.011000000 -0.13000 1
CW 12.011000000 -0.13000 1
NA 14.006740000 0.15000 1
HCR 1.007940000 0.21000 1
HCW 1.007940000 0.21000 1
HCW 1.007940000 0.21000 1
C1 12.011000000 -0.17000 1
H1 1.007940000 0.13000 1
H1 1.007940000 0.13000 1
H1 1.007940000 0.13000 1
C1 12.011000000 -0.17000 1
H1 1.007940000 0.13000 1
H1 1.007940000 0.13000 1
C2 12.011000000 -0.05000 1
HC 1.007940000 0.06000 1
HC 1.007940000 0.06000 1
HC 1.007940000 0.06000 1
bonds 8
harm 1 2 3992.00000 1.3150
harm 1 5 3992.00000 1.3150
harm 2 3 3574.00000 1.3780
harm 5 4 3574.00000 1.3780
harm 2 9 2820.00000 1.4660
harm 5 13 2820.00000 1.4660
harm 3 4 4352.00000 1.3410
harm 13 16 2242.00000 1.5290
constrains 11
1 6 1.080000
4 8 1.080000
:
:
:
</pre>
*Explanation of above snapshot:
[[File:Wiki1.png|thumb|center|1100px]]

*scrolling down...
<pre>
:
:
:
angles 33
harm 5 1 2 585.20 109.8000
harm 6 1 2 292.60 125.1000
harm 6 1 5 292.60 125.1000
harm 1 2 3 585.20 108.0000
harm 1 5 4 585.20 108.0000
harm 2 3 7 292.60 122.0000
harm 5 4 8 292.60 122.0000
harm 2 3 4 585.20 107.1000
harm 5 4 3 585.20 107.1000
harm 8 4 3 292.60 130.9000
:
:
:
</pre>
*Explanation of above snapshot:
[[File:Wiki2.png|thumb|center|800px]]

*scrolling down more...
<pre>
:
:
:
dihedrals 46
cos3 6 1 2 9 0.000000 19.460000 0.000000 0.500000 0.500000
cos3 6 1 5 13 0.000000 19.460000 0.000000 0.500000 0.500000
cos3 6 1 2 3 0.000000 19.460000 0.000000 0.500000 0.500000
cos3 6 1 5 4 0.000000 19.460000 0.000000 0.500000 0.500000
cos3 1 2 3 7 0.000000 12.550000 0.000000 0.500000 0.500000
cos3 1 5 4 8 0.000000 12.550000 0.000000 0.500000 0.500000
:
:
:
</pre>
*Explanation of above snapshot:
Harmonic Dihedral Potential Vn/2 (1 + cos[nφ − γ]) from forcefield functional

*scrolling down even more...
<pre>
:
:
:
cos3 5 3 4 8 0.000000 9.200000 0.000000 0.500000 0.500000
cos3 2 4 3 7 0.000000 9.200000 0.000000 0.500000 0.500000
finish
alumcl
nummols 128
atoms 5
AL 26.9815400000 0.90920 1
CL 35.4530000000 -0.47730 4
bonds 4
harm 1 2 485.34000 2.1700
harm 1 3 485.34000 2.1700
harm 1 4 485.34000 2.1700
harm 1 5 485.34000 2.1700
angles 6
harm 3 1 2 209.20 109.5000
harm 4 1 2 209.20 109.5000
harm 5 1 2 209.20 109.5000
harm 4 1 3 209.20 109.5000
harm 5 1 3 209.20 109.5000
harm 5 1 4 209.20 109.5000
finish
vdW 66
CR CR lj 0.29288000 3.55000000
CR NA lj 0.45642051 3.39669000
CR CW lj 0.29288000 3.55000000
CR HCR lj 0.19173497 2.93104100
CR HCW lj 0.19173497 2.93104100
:
:
:
</pre>
*Explanation of above snapshot:
[[File:Wikiff4.png|thumb|center|900px]]
*Link to excel file with calculations for Lennard-Jones component [[Media:LJ-parameters.xlsx]]
*Link to PDF file for the whole input file FIELD [[Media:FIELD.pdf]]

==Notes==
<references/>

==References==
*[1] http://pubs.acs.org/doi/full/10.1021/jp014229s
*[2] http://pubs.acs.org/doi/abs/10.1021/jp9717655

Talk:Mod:Hunt Research Group/Wheretostart

2014-08-06T16:46:19Z

Jt413:

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

==Introduction==
Before any MD simulations can be run we require a suitable MM force field (potential function).
For Ionic Liquids there are several MM force fields available. In our work we currently use
the Imidazolium based IL FF of Can-Lopes et al.

==Specific example using [EMIM]+[AlCl4]-==
*For this example, we refer to these two articles for force field parameters<ref>J. D. Andrade, E. S. Boes, H. Stassen, J. Phys. Chem. B, 2002, 106, 3546-3548</ref><ref>T. Fox, P. A. Kollman, J. Phys. Chem. B, 1998, 102, 8070-8079</ref>.
*In the reported articles, the AMBER force field functional form for the potential energy V is used:
[[File:WikiLJ.png|thumb|center|400px]]

*Start with 3 input files: CONFIG, CONTROL and FIELD
*CONFIG gives your initial configuration (obtained from packmol and converted), CONTROL gives your parameters, and FIELD provides the force field
*Sample input file FIELD:
<pre>
EMIM-ALCl4 - JPCB 2002 v.106 p.3546
units kJ
molecules 2
EMIM
nummols 128
atoms 19
CR 12.011000000 -0.11000 1
NA 14.006740000 0.15000 1
CW 12.011000000 -0.13000 1
CW 12.011000000 -0.13000 1
NA 14.006740000 0.15000 1
HCR 1.007940000 0.21000 1
HCW 1.007940000 0.21000 1
HCW 1.007940000 0.21000 1
C1 12.011000000 -0.17000 1
H1 1.007940000 0.13000 1
H1 1.007940000 0.13000 1
H1 1.007940000 0.13000 1
C1 12.011000000 -0.17000 1
H1 1.007940000 0.13000 1
H1 1.007940000 0.13000 1
C2 12.011000000 -0.05000 1
HC 1.007940000 0.06000 1
HC 1.007940000 0.06000 1
HC 1.007940000 0.06000 1
bonds 8
harm 1 2 3992.00000 1.3150
harm 1 5 3992.00000 1.3150
harm 2 3 3574.00000 1.3780
harm 5 4 3574.00000 1.3780
harm 2 9 2820.00000 1.4660
harm 5 13 2820.00000 1.4660
harm 3 4 4352.00000 1.3410
harm 13 16 2242.00000 1.5290
constrains 11
1 6 1.080000
4 8 1.080000
:
:
:
</pre>
*Explanation of above snapshot:
[[File:Wiki1.png|thumb|center|1100px]]

*scrolling down...
<pre>
:
:
:
angles 33
harm 5 1 2 585.20 109.8000
harm 6 1 2 292.60 125.1000
harm 6 1 5 292.60 125.1000
harm 1 2 3 585.20 108.0000
harm 1 5 4 585.20 108.0000
harm 2 3 7 292.60 122.0000
harm 5 4 8 292.60 122.0000
harm 2 3 4 585.20 107.1000
harm 5 4 3 585.20 107.1000
harm 8 4 3 292.60 130.9000
:
:
:
</pre>
*Explanation of above snapshot:
[[File:Wiki2.png|thumb|center|800px]]

*scrolling down more...
<pre>
:
:
:
dihedrals 46
cos3 6 1 2 9 0.000000 19.460000 0.000000 0.500000 0.500000
cos3 6 1 5 13 0.000000 19.460000 0.000000 0.500000 0.500000
cos3 6 1 2 3 0.000000 19.460000 0.000000 0.500000 0.500000
cos3 6 1 5 4 0.000000 19.460000 0.000000 0.500000 0.500000
cos3 1 2 3 7 0.000000 12.550000 0.000000 0.500000 0.500000
cos3 1 5 4 8 0.000000 12.550000 0.000000 0.500000 0.500000
:
:
:
</pre>
*Explanation of above snapshot:
Harmonic Dihedral Potential Vn/2 (1 + cos[nφ − γ]) from forcefield functional

*scrolling down even more...
<pre>
:
:
:
cos3 5 3 4 8 0.000000 9.200000 0.000000 0.500000 0.500000
cos3 2 4 3 7 0.000000 9.200000 0.000000 0.500000 0.500000
finish
alumcl
nummols 128
atoms 5
AL 26.9815400000 0.90920 1
CL 35.4530000000 -0.47730 4
bonds 4
harm 1 2 485.34000 2.1700
harm 1 3 485.34000 2.1700
harm 1 4 485.34000 2.1700
harm 1 5 485.34000 2.1700
angles 6
harm 3 1 2 209.20 109.5000
harm 4 1 2 209.20 109.5000
harm 5 1 2 209.20 109.5000
harm 4 1 3 209.20 109.5000
harm 5 1 3 209.20 109.5000
harm 5 1 4 209.20 109.5000
finish
vdW 66
CR CR lj 0.29288000 3.55000000
CR NA lj 0.45642051 3.39669000
CR CW lj 0.29288000 3.55000000
CR HCR lj 0.19173497 2.93104100
CR HCW lj 0.19173497 2.93104100
:
:
:
</pre>
*Explanation of above snapshot:
[[File:Wikiff4.png|thumb|center|900px]]
*Link to excel file with calculations for Lennard-Jones component [[Media:LJ-parameters.xlsx]]
*Link to PDF file for the whole input file FIELD [[Media:FIELD.pdf]]

==Notes==
<references/>

==References==
*[1] http://pubs.acs.org/doi/full/10.1021/jp014229s
*[2] http://pubs.acs.org/doi/abs/10.1021/jp9717655

File:LJ-parameters.xlsx

2014-08-06T16:42:29Z

Jt413:

File:FIELD.pdf

2014-08-06T16:40:41Z

Jt413:

Talk:Mod:Hunt Research Group/Wheretostart

2014-08-06T15:47:43Z

Jt413: /* Notes */

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

==Introduction==
Before any MD simulations can be run we require a suitable MM force field (potential function).
For Ionic Liquids there are several MM force fields available. In our work we currently use
the Imidazolium based IL FF of Can-Lopes et al.

==Specific example using [EMIM]+[AlCl4]-==
*For this example, we refer to these two articles for force field parameters<ref>J. D. Andrade, E. S. Boes, H. Stassen, J. Phys. Chem. B, 2002, 106, 3546-3548</ref><ref>T. Fox, P. A. Kollman, J. Phys. Chem. B, 1998, 102, 8070-8079</ref>.
*In the reported articles, the AMBER force field functional form for the potential energy V is used:
[[File:WikiLJ.png|thumb|center|400px]]

*Start with 3 input files: CONFIG, CONTROL and FIELD
*CONFIG gives your initial configuration (obtained from packmol and converted), CONTROL gives your parameters, and FIELD provides the force field
*Sample input file FIELD:
<pre>
EMIM-ALCl4 - JPCB 2002 v.106 p.3546
units kJ
molecules 2
EMIM
nummols 128
atoms 19
CR 12.011000000 -0.11000 1
NA 14.006740000 0.15000 1
CW 12.011000000 -0.13000 1
CW 12.011000000 -0.13000 1
NA 14.006740000 0.15000 1
HCR 1.007940000 0.21000 1
HCW 1.007940000 0.21000 1
HCW 1.007940000 0.21000 1
C1 12.011000000 -0.17000 1
H1 1.007940000 0.13000 1
H1 1.007940000 0.13000 1
H1 1.007940000 0.13000 1
C1 12.011000000 -0.17000 1
H1 1.007940000 0.13000 1
H1 1.007940000 0.13000 1
C2 12.011000000 -0.05000 1
HC 1.007940000 0.06000 1
HC 1.007940000 0.06000 1
HC 1.007940000 0.06000 1
bonds 8
harm 1 2 3992.00000 1.3150
harm 1 5 3992.00000 1.3150
harm 2 3 3574.00000 1.3780
harm 5 4 3574.00000 1.3780
harm 2 9 2820.00000 1.4660
harm 5 13 2820.00000 1.4660
harm 3 4 4352.00000 1.3410
harm 13 16 2242.00000 1.5290
constrains 11
1 6 1.080000
4 8 1.080000
:
:
:
</pre>
*Explanation of above snapshot:
[[File:Wiki1.png|thumb|center|1100px]]

*scrolling down...
<pre>
:
:
:
angles 33
harm 5 1 2 585.20 109.8000
harm 6 1 2 292.60 125.1000
harm 6 1 5 292.60 125.1000
harm 1 2 3 585.20 108.0000
harm 1 5 4 585.20 108.0000
harm 2 3 7 292.60 122.0000
harm 5 4 8 292.60 122.0000
harm 2 3 4 585.20 107.1000
harm 5 4 3 585.20 107.1000
harm 8 4 3 292.60 130.9000
:
:
:
</pre>
*Explanation of above snapshot:
[[File:Wiki2.png|thumb|center|800px]]

*scrolling down more...
<pre>
:
:
:
dihedrals 46
cos3 6 1 2 9 0.000000 19.460000 0.000000 0.500000 0.500000
cos3 6 1 5 13 0.000000 19.460000 0.000000 0.500000 0.500000
cos3 6 1 2 3 0.000000 19.460000 0.000000 0.500000 0.500000
cos3 6 1 5 4 0.000000 19.460000 0.000000 0.500000 0.500000
cos3 1 2 3 7 0.000000 12.550000 0.000000 0.500000 0.500000
cos3 1 5 4 8 0.000000 12.550000 0.000000 0.500000 0.500000
:
:
:
</pre>
*Explanation of above snapshot:
Harmonic Dihedral Potential Vn/2 (1 + cos[nφ − γ]) from forcefield functional

*scrolling down even more...
<pre>
:
:
:
cos3 5 3 4 8 0.000000 9.200000 0.000000 0.500000 0.500000
cos3 2 4 3 7 0.000000 9.200000 0.000000 0.500000 0.500000
finish
alumcl
nummols 128
atoms 5
AL 26.9815400000 0.90920 1
CL 35.4530000000 -0.47730 4
bonds 4
harm 1 2 485.34000 2.1700
harm 1 3 485.34000 2.1700
harm 1 4 485.34000 2.1700
harm 1 5 485.34000 2.1700
angles 6
harm 3 1 2 209.20 109.5000
harm 4 1 2 209.20 109.5000
harm 5 1 2 209.20 109.5000
harm 4 1 3 209.20 109.5000
harm 5 1 3 209.20 109.5000
harm 5 1 4 209.20 109.5000
finish
vdW 66
CR CR lj 0.29288000 3.55000000
CR NA lj 0.45642051 3.39669000
CR CW lj 0.29288000 3.55000000
CR HCR lj 0.19173497 2.93104100
CR HCW lj 0.19173497 2.93104100
:
:
:
</pre>
*Explanation of above snapshot:
[[File:Wikiff4.png|thumb|center|900px]]

==Notes==
<references/>

==References==
*[1] http://pubs.acs.org/doi/full/10.1021/jp014229s
*[2] http://pubs.acs.org/doi/abs/10.1021/jp9717655

Talk:Mod:Hunt Research Group/Wheretostart

2014-08-06T15:46:40Z

Jt413:

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

==Introduction==
Before any MD simulations can be run we require a suitable MM force field (potential function).
For Ionic Liquids there are several MM force fields available. In our work we currently use
the Imidazolium based IL FF of Can-Lopes et al.

==Specific example using [EMIM]+[AlCl4]-==
*For this example, we refer to these two articles for force field parameters<ref>J. D. Andrade, E. S. Boes, H. Stassen, J. Phys. Chem. B, 2002, 106, 3546-3548</ref><ref>T. Fox, P. A. Kollman, J. Phys. Chem. B, 1998, 102, 8070-8079</ref>.
*In the reported articles, the AMBER force field functional form for the potential energy V is used:
[[File:WikiLJ.png|thumb|center|400px]]

*Start with 3 input files: CONFIG, CONTROL and FIELD
*CONFIG gives your initial configuration (obtained from packmol and converted), CONTROL gives your parameters, and FIELD provides the force field
*Sample input file FIELD:
<pre>
EMIM-ALCl4 - JPCB 2002 v.106 p.3546
units kJ
molecules 2
EMIM
nummols 128
atoms 19
CR 12.011000000 -0.11000 1
NA 14.006740000 0.15000 1
CW 12.011000000 -0.13000 1
CW 12.011000000 -0.13000 1
NA 14.006740000 0.15000 1
HCR 1.007940000 0.21000 1
HCW 1.007940000 0.21000 1
HCW 1.007940000 0.21000 1
C1 12.011000000 -0.17000 1
H1 1.007940000 0.13000 1
H1 1.007940000 0.13000 1
H1 1.007940000 0.13000 1
C1 12.011000000 -0.17000 1
H1 1.007940000 0.13000 1
H1 1.007940000 0.13000 1
C2 12.011000000 -0.05000 1
HC 1.007940000 0.06000 1
HC 1.007940000 0.06000 1
HC 1.007940000 0.06000 1
bonds 8
harm 1 2 3992.00000 1.3150
harm 1 5 3992.00000 1.3150
harm 2 3 3574.00000 1.3780
harm 5 4 3574.00000 1.3780
harm 2 9 2820.00000 1.4660
harm 5 13 2820.00000 1.4660
harm 3 4 4352.00000 1.3410
harm 13 16 2242.00000 1.5290
constrains 11
1 6 1.080000
4 8 1.080000
:
:
:
</pre>
*Explanation of above snapshot:
[[File:Wiki1.png|thumb|center|1100px]]

*scrolling down...
<pre>
:
:
:
angles 33
harm 5 1 2 585.20 109.8000
harm 6 1 2 292.60 125.1000
harm 6 1 5 292.60 125.1000
harm 1 2 3 585.20 108.0000
harm 1 5 4 585.20 108.0000
harm 2 3 7 292.60 122.0000
harm 5 4 8 292.60 122.0000
harm 2 3 4 585.20 107.1000
harm 5 4 3 585.20 107.1000
harm 8 4 3 292.60 130.9000
:
:
:
</pre>
*Explanation of above snapshot:
[[File:Wiki2.png|thumb|center|800px]]

*scrolling down more...
<pre>
:
:
:
dihedrals 46
cos3 6 1 2 9 0.000000 19.460000 0.000000 0.500000 0.500000
cos3 6 1 5 13 0.000000 19.460000 0.000000 0.500000 0.500000
cos3 6 1 2 3 0.000000 19.460000 0.000000 0.500000 0.500000
cos3 6 1 5 4 0.000000 19.460000 0.000000 0.500000 0.500000
cos3 1 2 3 7 0.000000 12.550000 0.000000 0.500000 0.500000
cos3 1 5 4 8 0.000000 12.550000 0.000000 0.500000 0.500000
:
:
:
</pre>
*Explanation of above snapshot:
Harmonic Dihedral Potential Vn/2 (1 + cos[nφ − γ]) from forcefield functional

*scrolling down even more...
<pre>
:
:
:
cos3 5 3 4 8 0.000000 9.200000 0.000000 0.500000 0.500000
cos3 2 4 3 7 0.000000 9.200000 0.000000 0.500000 0.500000
finish
alumcl
nummols 128
atoms 5
AL 26.9815400000 0.90920 1
CL 35.4530000000 -0.47730 4
bonds 4
harm 1 2 485.34000 2.1700
harm 1 3 485.34000 2.1700
harm 1 4 485.34000 2.1700
harm 1 5 485.34000 2.1700
angles 6
harm 3 1 2 209.20 109.5000
harm 4 1 2 209.20 109.5000
harm 5 1 2 209.20 109.5000
harm 4 1 3 209.20 109.5000
harm 5 1 3 209.20 109.5000
harm 5 1 4 209.20 109.5000
finish
vdW 66
CR CR lj 0.29288000 3.55000000
CR NA lj 0.45642051 3.39669000
CR CW lj 0.29288000 3.55000000
CR HCR lj 0.19173497 2.93104100
CR HCW lj 0.19173497 2.93104100
:
:
:
</pre>
*Explanation of above snapshot:
[[File:Wikiff4.png|thumb|center|900px]]

==Notes==
<references/>
{{Reflist}}

==References==
*[1] http://pubs.acs.org/doi/full/10.1021/jp014229s
*[2] http://pubs.acs.org/doi/abs/10.1021/jp9717655

File:Wikiff4.png

2014-08-06T15:43:05Z

Jt413:

File:Wikiff 3.png

2014-08-06T15:41:59Z

Jt413:

Talk:Mod:Hunt Research Group/Wheretostart

2014-08-06T15:40:31Z

Jt413:

Talk:Mod:Hunt Research Group/Wheretostart

2014-08-06T15:29:07Z

Jt413:

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

==In the Beginning==
Before any MD simulations can be run we require a suitable MM force field (potential function).
For Ionic Liquids there are several MM force fields available. In our work we currently use
the Imidazolium based IL FF of Can-Lopes et al.

==Specific example using [EMIM]+[AlCl4]-==
*For this example, we refer to these two articles for force field parameters<ref>J. D. Andrade, E. S. Boes, H. Stassen, J. Phys. Chem. B, 2002, 106, 3546-3548</ref><ref>T. Fox, P. A. Kollman, J. Phys. Chem. B, 1998, 102, 8070-8079</ref>.
*In the reported articles, the AMBER force field functional form for the potential energy V is used:
[[File:WikiLJ.png|thumb|center|400px]]

*Start with 3 input files: CONFIG, CONTROL and FIELD
*CONFIG gives your initial configuration (obtained from packmol and converted), CONTROL gives your parameters, and FIELD provides the force field
*Sample input file FIELD:
<pre>
EMIM-ALCl4 - JPCB 2002 v.106 p.3546
units kJ
molecules 2
EMIM
nummols 128
atoms 19
CR 12.011000000 -0.11000 1
NA 14.006740000 0.15000 1
CW 12.011000000 -0.13000 1
CW 12.011000000 -0.13000 1
NA 14.006740000 0.15000 1
HCR 1.007940000 0.21000 1
HCW 1.007940000 0.21000 1
HCW 1.007940000 0.21000 1
C1 12.011000000 -0.17000 1
H1 1.007940000 0.13000 1
H1 1.007940000 0.13000 1
H1 1.007940000 0.13000 1
C1 12.011000000 -0.17000 1
H1 1.007940000 0.13000 1
H1 1.007940000 0.13000 1
C2 12.011000000 -0.05000 1
HC 1.007940000 0.06000 1
HC 1.007940000 0.06000 1
HC 1.007940000 0.06000 1
bonds 8
harm 1 2 3992.00000 1.3150
harm 1 5 3992.00000 1.3150
harm 2 3 3574.00000 1.3780
harm 5 4 3574.00000 1.3780
harm 2 9 2820.00000 1.4660
harm 5 13 2820.00000 1.4660
harm 3 4 4352.00000 1.3410
harm 13 16 2242.00000 1.5290
constrains 11
1 6 1.080000
4 8 1.080000
:
:
:
</pre>
*Explanation of above snapshot:
[[File:Wiki1.png|thumb|center|1100px]]

*scrolling down...
<pre>
:
:
:
angles 33
harm 5 1 2 585.20 109.8000
harm 6 1 2 292.60 125.1000
harm 6 1 5 292.60 125.1000
harm 1 2 3 585.20 108.0000
harm 1 5 4 585.20 108.0000
harm 2 3 7 292.60 122.0000
harm 5 4 8 292.60 122.0000
harm 2 3 4 585.20 107.1000
harm 5 4 3 585.20 107.1000
harm 8 4 3 292.60 130.9000
:
:
:
</pre>
*Explanation of above snapshot:
[[File:Wiki2.png|thumb|center|800px]]

==Notes==
<references/>
{{Reflist}}

==References==
*[1] http://pubs.acs.org/doi/full/10.1021/jp014229s
*[2] http://pubs.acs.org/doi/abs/10.1021/jp9717655

File:Wiki2.png

2014-08-06T15:24:27Z

Jt413:

File:Wiki1.png

2014-08-06T15:15:37Z

Jt413:

Talk:Mod:Hunt Research Group/Wheretostart

2014-08-06T15:15:04Z

Jt413:

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

==In the Beginning==
Before any MD simulations can be run we require a suitable MM force field (potential function).
For Ionic Liquids there are several MM force fields available. In our work we currently use
the Imidazolium based IL FF of Can-Lopes et al.

==Specific example using [EMIM]+[AlCl4]-==
*For this example, we refer to these two articles for force field parameters<ref>J. D. Andrade, E. S. Boes, H. Stassen, J. Phys. Chem. B, 2002, 106, 3546-3548</ref><ref>T. Fox, P. A. Kollman, J. Phys. Chem. B, 1998, 102, 8070-8079</ref>.
*In the reported articles, the AMBER force field functional form for the potential energy V is used:
[[File:WikiLJ.png|thumb|center|400px]]
<pre>
EMIM-ALCl4 - JPCB 2002 v.106 p.3546
units kJ
molecules 2
EMIM
nummols 128
atoms 19
CR 12.011000000 -0.11000 1
NA 14.006740000 0.15000 1
CW 12.011000000 -0.13000 1
CW 12.011000000 -0.13000 1
NA 14.006740000 0.15000 1
HCR 1.007940000 0.21000 1
HCW 1.007940000 0.21000 1
HCW 1.007940000 0.21000 1
C1 12.011000000 -0.17000 1
H1 1.007940000 0.13000 1
H1 1.007940000 0.13000 1
H1 1.007940000 0.13000 1
C1 12.011000000 -0.17000 1
H1 1.007940000 0.13000 1
H1 1.007940000 0.13000 1
C2 12.011000000 -0.05000 1
HC 1.007940000 0.06000 1
HC 1.007940000 0.06000 1
HC 1.007940000 0.06000 1
bonds 8
harm 1 2 3992.00000 1.3150
harm 1 5 3992.00000 1.3150
harm 2 3 3574.00000 1.3780
harm 5 4 3574.00000 1.3780
harm 2 9 2820.00000 1.4660
harm 5 13 2820.00000 1.4660
harm 3 4 4352.00000 1.3410
harm 13 16 2242.00000 1.5290
constrains 11
1 6 1.080000
4 8 1.080000
</pre>

==Notes==
<references/>
{{Reflist}}

==References==
*[1] http://pubs.acs.org/doi/full/10.1021/jp014229s
*[2] http://pubs.acs.org/doi/abs/10.1021/jp9717655

File:WikiLJ.png

2014-08-06T15:10:09Z

Jt413: uploaded a new version of "File:WikiLJ.png"

File:WikiLJ.png

2014-08-06T15:02:51Z

Jt413: LJ

Talk:Mod:Hunt Research Group/Wheretostart

2014-08-06T15:02:25Z

Jt413:

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

==In the Beginning==
Before any MD simulations can be run we require a suitable MM force field (potential function).
For Ionic Liquids there are several MM force fields available. In our work we currently use
the Imidazolium based IL FF of Can-Lopes et al.
[[File:ForceFields.png]]

==Specific example using [EMIM]+[AlCl4]-==
*For this example, we refer to these two articles for force field parameters<ref>J. D. Andrade, E. S. Boes, H. Stassen, J. Phys. Chem. B, 2002, 106, 3546-3548</ref><ref>T. Fox, P. A. Kollman, J. Phys. Chem. B, 1998, 102, 8070-8079</ref>.
*In the reported articles, the AMBER force field functional form for the potential energy V is used:

<pre>
EMIM-ALCl4 - JPCB 2002 v.106 p.3546
units kJ
molecules 2
EMIM
nummols 128
atoms 19
CR 12.011000000 -0.11000 1
NA 14.006740000 0.15000 1
CW 12.011000000 -0.13000 1
CW 12.011000000 -0.13000 1
NA 14.006740000 0.15000 1
HCR 1.007940000 0.21000 1
HCW 1.007940000 0.21000 1
HCW 1.007940000 0.21000 1
C1 12.011000000 -0.17000 1
H1 1.007940000 0.13000 1
H1 1.007940000 0.13000 1
H1 1.007940000 0.13000 1
C1 12.011000000 -0.17000 1
H1 1.007940000 0.13000 1
H1 1.007940000 0.13000 1
C2 12.011000000 -0.05000 1
HC 1.007940000 0.06000 1
HC 1.007940000 0.06000 1
HC 1.007940000 0.06000 1
bonds 8
harm 1 2 3992.00000 1.3150
harm 1 5 3992.00000 1.3150
harm 2 3 3574.00000 1.3780
harm 5 4 3574.00000 1.3780
harm 2 9 2820.00000 1.4660
harm 5 13 2820.00000 1.4660
harm 3 4 4352.00000 1.3410
harm 13 16 2242.00000 1.5290
constrains 11
1 6 1.080000
4 8 1.080000
</pre>

==Notes==
<references/>
{{Reflist}}

==References==
*[1] http://pubs.acs.org/doi/full/10.1021/jp014229s
*[2] http://pubs.acs.org/doi/abs/10.1021/jp9717655

Talk:Mod:Hunt Research Group/Wheretostart

2014-08-06T14:29:07Z

Jt413:

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

#In the Beginning

Before any MD simulations can be run we require a suitable MM force field (potential function).
For Ionic Liquids there are several MM force fields available. In our work we currently use
the Imidazolium based IL FF of Can-Lopes et al.
[[File:ForceFields.png]]

Talk:Mod:Hunt Research Group/Wheretostart

2014-08-06T14:18:01Z

Jt413:

#In the Beginning

Before any MD simulations can be run we require a suitable MM force field (potential function).
For Ionic Liquids there are several MM force fields available. In our work we currently use
the Imidazolium based IL FF of Can-Lopes et al.
[[File:ForceFields.png]]

File:ForceFields.png

2014-08-06T14:17:33Z

Jt413:

File:Wiki.png

2014-08-06T14:17:12Z

Jt413: uploaded a new version of "File:Wiki.png": Reverted to version as of 13:29, 24 March 2006

Talk:Mod:Hunt Research Group/Wheretostart

2014-08-06T14:14:30Z

Jt413:

File:Wiki.png

2014-08-06T14:12:45Z

Jt413: uploaded a new version of "File:Wiki.png"

Talk:Mod:Hunt Research Group/Wheretostart

2014-08-06T14:10:46Z

Jt413:

Mod:Hunt Research Group/calendar

2014-07-24T09:01:57Z

Jt413:

== 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 jacq away </td>
<td bgcolor="#CCCCCC">26th jacq away </td>
<td bgcolor="#CCCCCC">27th jacq away </td>
</tr>
<tr valign="top">
<td>28th Matthew Away jacq 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

2014-07-22T16:27:39Z

Jt413:

== 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 jacq away </td>
<td bgcolor="#CCCCCC">26th jacq away </td>
<td bgcolor="#CCCCCC">27th jacq away </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>