Where are your LJ parameters? Are you sure that Tsuzuki uses all standard OPLS parameters?
What density do you get in your simulation? -- Dr. Vitaly V. Chaban, Department of Chemistry University of Rochester, Rochester, New York 14627-0216 On Mon, May 2, 2011 at 1:59 AM, Prema Awati <prem...@iiserpune.ac.in> wrote: > 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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