[gmx-users] Help about Table.xvg

[kun jiao]

Thanks David:)



On 12/1/05, David van der Spoel <spoel at xray.bmc.uu.se> wrote:
>
> kun jiao wrote:
> > Thanks, David. I look into this file, and I know I need to set vdwtype =
> > user in *.mdp file.
> >  But I still don't know how to set [ nonbond_parms ] in force field
> file,
> >  which relate this table.xvg with two atoms type.
> > This is my force field file. Could you tell me how to modify it to
> > specify CH3 CH3 interaction as vdw potential in table.xvg
> >
> > -----------------------------------------------------------------------
> > [ defaults ]
> > 1       1
> > [ atomtypes ]
> > ;name     mass     charge ptype  c6           c12
> > ;
> >   CH3    14.0000    0.000  A 2.36400e-03 1.59000e-06
> >
> >
> > [ nonbond_params ]
> >   ; i    j    func    c6           c12
> >   CH3   CH3     1 2.36400e-03  1.59000e-06
>
> This is fine with the normal table6_12
>
> >
> ----------------------------------------------------------------------------------------------
> >
> > On 12/1/05, *David van der Spoel* < spoel at xray.bmc.uu.se
> > <mailto:spoel at xray.bmc.uu.se>> wrote:
> >
> >     kun jiao wrote:
> >
> >      > Dear, Gromacs Community,
> >      >     I am a new user of Gromacs. In my project I need to implement
> a
> >      > very complicate vdw potential. I read the gromacs manual which
> said I
> >      > need to prepare a table.xvg file.
> >      > But I have no idea how this file looks like, and how to relate it
> >     with
> >      > top file ( how to specify nonbond_params ). Could anyone give me
> an
> >      > example, such as table.xvg, *.top,  *.itp ?.
> >
> >
> >     in share/top you will find 6-12 etc. tables.
> >     Basically you need
> >     x fc(x) fc"(x) fd(x) fd"(x) fr(x) fr"(x)
> >     fc(x) will be multiplied by charges
> >     fd(x) by dispersion constant (C6)
> >     fr(x) by repulsion constant (C12)
> >
> >      > Any suggestion is appreciate:)
> >      >
> >      > Regards,
> >      > Kun
> >      >
>
> >      >------------------------------------------------------------------------
> >
> >      >
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> >
> >
> >     --
> >     David.
> >
> ________________________________________________________________________
> >     David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
> >     Dept. of Cell and Molecular Biology, Uppsala University.
> >     Husargatan 3, Box 596,          75124 Uppsala, Sweden
> >     phone:  46 18 471 4205          fax: 46 18 511 755
> >     spoel at xray.bmc.uu.se
> >     <mailto:spoel at xray.bmc.uu.se>    spoel at gromacs.org
> >     <mailto:spoel at gromacs.org>   http://xray.bmc.uu.se/~spoel
> >
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> >
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>
> --
> David.
> ________________________________________________________________________
> David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
> Dept. of Cell and Molecular Biology, Uppsala University.
> Husargatan 3, Box 596,          75124 Uppsala, Sweden
> phone:  46 18 471 4205          fax: 46 18 511 755
> spoel at xray.bmc.uu.se    spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
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