[gmx-users] virtual sites

[Sikandar Mashayak]

you can do it as following

1. create index file make_indx -f conf.gro -n index.ndx ( select VS and any
other atoms you want lets say OTHERS)
2. in .mdp define energygrps "VS OTHERS"
3. exclude interactions by specifying energygrp_excl VS OTHERS in .mdp file

for more you can refer to manual..

I hope it helps

--
sikandar



On Thu, May 5, 2011 at 11:00 AM, Gavin Melaugh <gmelaugh01 at qub.ac.uk> wrote:

> Hi Sikandar
>
> Cheers. How do you actually define the energy groups?
>
> Gavin
>
> Sikandar Mashayak wrote:
> > yes, you can make virtual sites interact with only specific sites by
> > using Energy Exclusion between energy groups. This can be done by
> > defining energy groups for virtual sites and other atoms, then exclude
> > or include the non-bonded interactions between them accordingly...
> >
> > On Thu, May 5, 2011 at 7:30 AM, Gavin Melaugh <gmelaugh01 at qub.ac.uk
> > <mailto:gmelaugh01 at qub.ac.uk>> wrote:
> >
> >     Hi All
> >
> >     Is it possible to have a virtual site interact with only specific
> >     atoms
> >     and not interact at all with everything else?
> >
> >
> >     Cheers
> >
> >     Gavin
> >     --
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