[gmx-users] Fw: Re: Re: ionic liquids
Dommert Florian
dommert at icp.uni-stuttgart.de
Tue May 3 11:32:48 CEST 2011
if you haven't changed anything in the ffoplsaa force field files of
gromacs I do not think that you have the correct parametrization. You
wether have to define the short range parameters on the top file or you
change the ffoplsaa files and insert the parameters of Tsuzuki. How how
do this can be found in the manual.
/Flo
On Tue, 2011-05-03 at 11:36 +0530, Prema Awati wrote:
>
>
> -- Original Message --
> From: prema.a at iiserpune.ac.in
> To: vvchaban at gmail.com
> Date: Tue, 3 May 2011 11:30:00 +0530 (GMT+05:30)
> Subject: Re: Re: ionic liquids
>
> Sir,
>
> Thanks for your response !!
>
> 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.
>
> Tsuzuki et.al used basically Lopes et.al forcefield which was
> refined(partial charges,nonbonding parameters ) to reproduce
> experimental density.
>
> 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.
>
> Thanks.
>
>
> -- Original Message --
> From: Vitaly Chaban <vvchaban at gmail.com>
> To: Prema Awati <prema.a at iiserpune.ac.in>
> Cc: gmx-users at gromacs.org
> Date: Mon, 2 May 2011 15:00:19 -0400
> Subject: Re: ionic liquids
>
> 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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--
Florian Dommert
Dipl. - Phys.
Institute for Computational Physics
University Stuttgart
Pfaffenwaldring 27
70569 Stuttgart
EMail: dommert at icp.uni-stuttgart.de
Homepage: http://www.icp.uni-stuttgart.de/~icp/Florian_Dommert
Tel.: +49 - (0)711 - 68563613
Fax.: +49 - (0)711 - 68563658
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