Where are your LJ parameters? <div><br></div><div>Are you sure that Tsuzuki uses all standard OPLS parameters?</div><div><br></div><div>What density do you get in your simulation?<br><div><br></div><div><br>-- <br>Dr. Vitaly V. Chaban, Department of Chemistry<br>
University of Rochester, Rochester, New York 14627-0216</div><div><br></div><div><br></div><div><br><br><div class="gmail_quote">On Mon, May 2, 2011 at 1:59 AM, Prema Awati <span dir="ltr"><<a href="mailto:prema.a@iiserpune.ac.in">prema.a@iiserpune.ac.in</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;"><div> 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>
</div></blockquote></div>
</div></div>