[gmx-users] Re: ionic liquids
Vitaly Chaban
vvchaban at gmail.com
Mon May 2 21:00:19 CEST 2011
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 <prema.a at 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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