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

Gavin Melaugh gmelaugh01 at qub.ac.uk
Fri May 6 14:20:41 CEST 2011

O.k Cheers
Justin A. Lemkul wrote:
> Gavin Melaugh wrote:
>> Yeah I see your point about the types. With regard to the initial
>> configuration state I would have assumed that gromacs knew the initial
>> position of the virtual site  when I stated that it was to be at the
>> COG  of the  3 atoms in  the [virtual_sitesn] directive.
> I believe this information is only used during mdrun to construct the
> position after forces have been applied and coordinates updated.  You
> can run a simple protein through pdb2gmx with -vsite hydrogens to see
> how all of this should be put together.
> -Justin

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