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<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: Tue, 3 May 2011 11:30:00 +0530 (GMT+05:30)<br >
Subject: Re: Re: ionic liquids<br >
<br >
Sir,<br >
<br >
Thanks for your response !!<br >
<br >
The LJ parameters are defined in forcefield database so it need not require to be mentioned in topology,I followed gromacs manual.But If its working by adding in the topology,then please guide me regarding LJ parameters. I used OPLS forcefield to create raw topology and then edited referring Tsuzuki"s.<br >
<br >
Tsuzuki et.al used basically Lopes et.al forcefield which was refined(partial charges,nonbonding parameters ) to reproduce experimental density.<br >
<br >
I obtained 1.0045 g/cm3 density which is poor to do final production run in order to study diffusive dynamics of ionic liquids, so I am looking to get exact density that of Tsuzuki.<br >
<br >
Thanks.<br >
<br >
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<font face="Arial" size="2"><font face="Arial" size="2"><b><i>-- Original Message --</i></b><br >
From: Vitaly Chaban <vvchaban@gmail.com><br >
To: Prema Awati <prema.a@iiserpune.ac.in><br >
Cc: gmx-users@gromacs.org<br >
Date: Mon, 2 May 2011 15:00:19 -0400<br >
Subject: Re: ionic liquids<br >
<br >
Where are your LJ parameters?</font> </font>
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<font face="Arial" size="2"><font face="Arial" size="2">Are you sure that Tsuzuki uses all standard OPLS parameters?</font></font></DIV>
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<font face="Arial" size="2"><font face="Arial" size="2">What density do you get in your simulation?</font><br >
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<font face="Arial" size="2"><font face="Arial" size="2">--<br >
Dr. Vitaly V. Chaban, Department of Chemistry<br >
University of Rochester, Rochester, New York 14627-0216</font></font></DIV>
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<DIV CLASS="gmail_quote">
<font face="Arial" size="2"><font face="Arial" size="2">On Mon, May 2, 2011 at 1:59 AM, Prema Awati <SPAN DIR="ltr"><<A TARGET="_blank" HREF="mailto:prema.a@iiserpune.ac.in" _CKE_SAVED_HREF="mailto:prema.a@iiserpune.ac.in">prema.a@iiserpune.ac.in</A>></SPAN> wrote:<br >
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<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
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<font face="Arial" size="2"><font face="Arial" size="2">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 >
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