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<font face="Arial" size="2"><b><i>-- Original Message --</i></b><br >
From: prema.a@iiserpune.ac.in<br >
To: gmx-users@gromacs.org<br >
Date: Mon, 2 May 2011 12:06:34 +0530 (GMT+05:30)<br >
Subject: Fw: ionic liquids<br >
<br >
<br >
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<font face="Arial" size="2"><font face="Arial" size="2"><b><i>-- Original Message --</i></b><br >
From: prema.a@iiserpune.ac.in<br >
To: vvchaban@gmail.com<br >
Date: Mon, 2 May 2011 11:29:44 +0530 (GMT+05:30)<br >
Subject: ionic liquids<br >
<br >
sir,<br >
I am grateful regarding your reply. The reported density for [bmim][bf4] system is 1.198 g/cm3.I was wondering whether you asked for the topology that I am using for my calculation or the one that Tsuzuki.et.al.(one I am referring) have used. Well, following is the toopology that I have created for my system.<br >
<br >
<br >
File 'bmim.top' was generated<br >
By user: onbekend (0)<br >
On host: onbekend<br >
At date: Fri Apr 15 18:03:14 2011<br >
<br >
This is a include topology file<br >
<br >
It was generated using program:<br >
Generated by x2top<br >
<br >
Command line was:<br >
g_x2top_d -f boxbmim.pdb -o bmim.top<br >
<br >
Force field was read from the standard Gromacs share directory.<br >
<br >
<br >
Include forcefield parameters<br >
#include "oplsaa.ff/forcefield.itp"<br >
<br >
[ moleculetype ]<br >
Name nrexcl<br >
BIM 3<br >
<br >
[ atoms ]<br >
nr type resnr residue atom cgnr charge mass typeB chargeB massB<br >
1 opls_557 1 BIM NA 1 0.24 14.0067 ; qtot 0.24<br >
2 opls_560 1 BIM CW 2 -0.16 12.011 ; qtot 0.74<br >
3 opls_561 1 BIM CW 3 -0.27 12.011 ; qtot 1.24<br >
4 opls_557 1 BIM NA 4 0.32 14.0067 ; qtot 1.48<br >
5 opls_558 1 BIM CR 5 -0.22 12.011 ; qtot 1.26<br >
6 opls_905 1 BIM C1 6 -0.35 12.011 ; qtot 0.91<br >
7 opls_908 1 BIM C1 7 -0.14 12.011 ; qtot 0.77<br >
8 opls_136 1 BIM C2 8 -0.12 12.011 ; qtot 0.65<br >
9 opls_136 1 BIM CS 9 -0.12 12.011 ; qtot 0.53<br >
10 opls_135 1 BIM CT 10 -0.18 12.011 ; qtot 0.35<br >
11 opls_565 1 BIM HA 2 0.23 1.008 ; qtot 0.41<br >
12 opls_564 1 BIM HA 3 0.27 1.008 ; qtot 0.47<br >
13 opls_563 1 BIM HA 5 0.25 1.008 ; qtot 0.53<br >
14 opls_911 1 BIM H1 6 0.17 1.008 ; qtot 0.59<br >
15 opls_911 1 BIM H1 6 0.17 1.008 ; qtot 0.65<br >
16 opls_911 1 BIM H1 6 0.17 1.008 ; qtot 0.71<br >
17 opls_911 1 BIM H1 7 0.16 1.008 ; qtot 0.77<br >
18 opls_911 1 BIM H1 7 0.16 1.008 ; qtot 0.83<br >
19 opls_140 1 BIM HC 8 0.06 1.008 ; qtot 0.89<br >
20 opls_140 1 BIM HC 8 0.06 1.008 ; qtot 0.95<br >
21 opls_140 1 BIM HC 9 0.06 1.008 ; qtot 1.01<br >
22 opls_140 1 BIM HC 9 0.06 1.008 ; qtot 1.07<br >
23 opls_140 1 BIM HC 10 0.06 1.008 ; qtot 1.13<br >
24 opls_140 1 BIM HC 10 0.06 1.008 ; qtot 1.19<br >
25 opls_140 1 BIM HC 10 0.06 1.008 ; qtot 1.25<br >
<br >
[ bonds ]<br >
ai aj funct c0 c1 c2 c3<br >
1 2 1 0.1372 178656.8<br >
1 5 1 0.1340 199576.8<br >
1 6 1 0.1466 141000.8<br >
2 3 1 0.1375 217568.0<br >
2 11 1 0.1080 138490.4<br >
3 4 1 0.1372 178656.8<br >
3 12 1 0.1080 138490.4<br >
4 5 1 0.1340 199576.8<br >
4 7 1 0.1466 141000.8<br >
5 13 1 0.1080 138490.4<br >
6 14 1 0.1090 138490.4<br >
6 15 1 0.1090 138490.4<br >
6 16 1 0.1090 138490.4<br >
7 8 1 0.1516 112131.2<br >
7 17 1 0.1090 138490.4<br >
7 18 1 0.1090 138490.4<br >
8 9 1 0.1529 112131.2<br >
8 19 1 0.1090 138490.4<br >
8 20 1 0.1090 138490.4<br >
9 10 1 0.1529 112131.2<br >
9 21 1 0.1090 138490.4<br >
9 22 1 0.1090 138490.4<br >
10 23 1 0.1090 138490.4<br >
10 24 1 0.1090 138490.4<br >
10 25 1 0.1090 138490.4<br >
<br >
[ pairs ]<br >
ai aj funct c0 c1 c2 c3<br >
1 7 1<br >
1 12 1<br >
2 7 1<br >
2 13 1<br >
2 14 1<br >
2 15 1<br >
2 16 1<br >
3 6 1<br >
3 8 1<br >
3 13 1<br >
3 17 1<br >
3 18 1<br >
4 6 1<br >
4 9 1<br >
4 11 1<br >
4 19 1<br >
4 20 1<br >
5 8 1<br >
5 11 1<br >
5 12 1<br >
5 14 1<br >
5 15 1<br >
5 16 1<br >
5 17 1<br >
5 18 1<br >
6 11 1<br >
6 13 1<br >
7 10 1<br >
7 12 1<br >
7 13 1<br >
7 21 1<br >
7 22 1<br >
8 23 1<br >
8 24 1<br >
8 25 1<br >
9 17 1<br >
9 18 1<br >
10 19 1<br >
10 20 1<br >
11 12 1<br >
17 19 1<br >
17 20 1<br >
18 19 1<br >
18 20 1<br >
19 21 1<br >
19 22 1<br >
20 21 1<br >
20 22 1<br >
21 23 1<br >
21 24 1<br >
21 25 1<br >
22 23 1<br >
22 24 1<br >
22 25 1<br >
<br >
[ angles ]<br >
ai aj ak funct c0 c1 c2 c3<br >
2 1 5 1 109.0 292.88<br >
2 1 6 1 125.6 292.88<br >
5 1 6 1 125.6 292.88<br >
1 2 3 1 107.1 292.88<br >
1 2 11 1 122.0 146.44<br >
3 2 11 1 130.9 146.44<br >
2 3 4 1 107.1 292.88<br >
2 3 12 1 130.9 146.44<br >
4 3 12 1 122.0 146.44<br >
3 4 5 1 109.0 292.88<br >
3 4 7 1 125.6 292.88<br >
5 4 7 1 125.6 292.88<br >
1 5 4 1 107.8 292.88<br >
1 5 13 1 126.1 146.44<br >
4 5 13 1 126.1 146.44<br >
1 6 14 1 107.2 156.61<br >
1 6 15 1 107.2 156.61<br >
1 6 16 1 107.2 156.61<br >
14 6 15 1 111.5 138.07<br >
14 6 16 1 111.5 138.07<br >
15 6 16 1 111.5 138.07<br >
4 7 8 1 110.7 418.40<br >
4 7 17 1 107.2 156.61<br >
4 7 18 1 107.2 156.61<br >
8 7 17 1 113.7 156.61<br >
8 7 18 1 113.7 156.61<br >
17 7 18 1 111.5 138.07<br >
7 8 9 1 111.4 418.40<br >
7 8 19 1 110.7 156.61<br >
7 8 20 1 110.7 156.61<br >
9 8 19 1 110.7 156.61<br >
9 8 20 1 110.7 156.61<br >
19 8 20 1 107.8 138.07<br >
8 9 10 1 112.0 418.40<br >
8 9 21 1 110.7 156.61<br >
8 9 22 1 110.7 156.61<br >
10 9 21 1 110.7 156.61<br >
10 9 22 1 110.7 156.61<br >
21 9 22 1 107.8 138.07<br >
9 10 23 1 110.7 156.61<br >
9 10 24 1 110.7 156.61<br >
9 10 25 1 110.7 156.61<br >
23 10 24 1 107.8 138.07<br >
23 10 25 1 107.8 138.07<br >
24 10 25 1 107.8 138.07<br >
[ dihedrals ]<br >
ai aj ak al funct c0 c1 c2 c3 c4 c5<br >
5 1 2 3 1 0.0 -12.5520 2<br >
2 1 5 4 1 0.0 -19.4598 2<br >
2 1 6 14 1 0.0 0.51882 3<br >
1 2 3 4 1 0.0 -44.9780 2<br >
2 3 4 5 1 0.0 -12.5520 2<br >
3 4 5 1 1 0.0 -19.4598 2<br >
3 4 7 8 1 0.0 -0.09205 1<br >
4 7 8 9 1 0.0 -10.9788 1<br >
7 8 9 10 1 0.0 4.44341 1<br >
8 9 10 23 1 0.0 1.53134 3<br >
#include "topbf4.itp"<br >
<br >
[ system ]<br >
Name<br >
BIM<br >
<br >
[ molecules ]<br >
Compound #mols<br >
BIM 125<br >
TFB 125<br >
<br >
<br >
<br >
<br >
<br >
<br >
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