[gmx-users] virtual sites

[Gavin Melaugh]

Hi Sikandar

Many Thanks for the reply. When you define energygrps in the mdp file,
does that mean that only these groups are written to the energy file. I
take it that all iother information regarding the energy is written as
well i.e if you left this section blank

Cheers

Gavin

Sikandar Mashayak wrote:
> 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
> <mailto: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>
>     > <mailto: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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