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

[Gavin Melaugh]

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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