[gmx-users] (no subject)
David van der Spoel
spoel at xray.bmc.uu.se
Wed Jul 17 04:27:53 CEST 2002
On Tue, 2002-07-16 at 15:29, Alan Wilter Sousa da Silva wrote:
> 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?
You want the ions to diffuse around freely, unless they are tightly
bound to the protein. Usually your inhibitor is also tightly bound.
Everything that should stick to the protein should be in one COM group,
while the rest (solvent + counter ions) should be in the other.
> 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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Dr. David van der Spoel, Biomedical center, Dept. of Biochemistry
Husargatan 3, Box 576, 75123 Uppsala, Sweden
phone: 46 18 471 4205 fax: 46 18 511 755
spoel at xray.bmc.uu.se spoel at gromacs.org http://zorn.bmc.uu.se/~spoel
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