[gmx-users] (no subject)

Alan Wilter Sousa da Silva alan at biof.ufrj.br
Tue Jul 16 15:29:59 CEST 2002

On 15 Jul 2002, David wrote:

> On Mon, 2002-07-15 at 20:26, J Lorieau wrote:
> > Hi,
> >
> > 	I have a simple question, unfortunately. I'm simulating 1A30 - HIV
> > protease in box of water. HIV PR is a dimer. After about 1 ns of
> > simulation, the protein COM drift out of the box.
> This is not a problem, but if you really don't want it to happen you can
> apply center-of-mass motion removal to your protein and solvent
> separately if you wish by specifying com-groups.

	I have a system with protein + inhibitor + ions + solvent, should
I apply so center-of-mass motion removal to each group in order to avoid
such COM drift?  Or just protein and solvent?
	The mdrun -rerun will not have result, won't it?

Many thanks in advance.

Alan Wilter S. da Silva
 Laboratório de Física Biológica
  Instituto de Biofísica Carlos Chagas Filho
   Universidade do Brasil/UFRJ
    Rio de Janeiro, Brasil

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