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
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