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