[gmx-users] Adding Virtual Site to the Molecule

[Mark Abraham]

On 15/04/2011 6:05 AM, Sikandar Mashayak wrote:
> Hi
>
> I am thinking of a simulation set up, where I modify a 
> structure/topology of a molecule under consideration, in which, I want 
> to introduce a dummy atom/site which will always be located at center 
> of mass of a molecule and it will only interact with dummy atom of 
> other molecule.

COM vsites are already implemented, see manual. To have them interact 
only with other such dummy atom(s) in other molecules, you will have to 
use energy groups and energy group exclusions. See manual.

Mark