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

[Sikandar Mashayak]

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> 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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