[gmx-users] virtual sites set up for topology file

[Sikandar Mashayak]

yes it will...

On Fri, May 6, 2011 at 11:02 AM, Gavin Melaugh <gmelaugh01 at qub.ac.uk> wrote:

> Cheers Sikandar
>
> I take it that because combination rule 3 (provide sigma and epsilon) is
> stated gromacs assumes that all values in nonbonding parameters are
> sigma and epsilon. I know this tp be tru for the atomtypes but does it
> filter down to all intermolecular interactions.
>
> Cheers
>
> Gavin
>
> Sikandar Mashayak wrote:
> > Yes, since sigma and epsilon are zero for VS then interactions between
> > and VS-VS and VS-(any other atom) would result in zero force. Since
> > you explicitly define the interaction between VS-C3, combination rule
> > won't be used and C6(VS_C3) and C12(VS_C3) will be computed as per
> > sigma(VS_C3) epsilon(VS_C3) you defined under [nonbond_params]
> >
> > cheers
> >
> > sikandar
> >
> > On Fri, May 6, 2011 at 9:03 AM, Gavin Melaugh <gmelaugh01 at qub.ac.uk
> > <mailto:gmelaugh01 at qub.ac.uk>> wrote:
> >
> >     Am I correct in saying now, from the following topology (exerpts),
> >     that
> >     the virtual site VS will only interact with C3?
> >     I guess I don't have to give the atom indices of this interaction
> >     in the
> >     pair list which I use only for 1_4 interactions?
> >     Can I use sigma and epsilon in the nonbond_params directive like in
> >     atomtypes.
> >
> >     ;Parameter level
> >     [defaults]
> >     ; nbfunc    comb-rule     gen-pairs        fudgeLJ     fudgeQQ
> >         1         3              yes            0.5         0.5
> >
> >     [atomtypes]
> >     ;type     mass           charge      ptype     sigma(nm)
> >     epsilon(kjmol-1)
> >       CB     12.011000      0.000000       A      0.355000      0.292880
> >       CA     12.011000     -0.115000       A      0.355000      0.292880
> >       HC      1.008000      0.115000       A      0.242000      0.125520
> >       CU     13.019000      0.265000       A      0.350000      0.334720
> >       NU     14.007000     -0.597000       A      0.325000      0.711280
> >       CH     13.019000      0.332000       A      0.385000      0.334720
> >       C3     15.035000      0.000000       A      0.390500      0.732200
> >       C2     14.027000      0.000000       A      0.390500      0.493712
> >       VS      0.0           0.0            V      0.0           0.0
> >
> >
> >     [nonbond_params]
> >     ;i    j      func     sigma    epsilon
> >     VS   C3        1       0.1     0.03153
> >
> >     --
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