[gmx-users] com motion
David van der Spoel
spoel at xray.bmc.uu.se
Wed Apr 9 11:34:01 CEST 2003
On Wed, 2003-04-09 at 11:13, Mustafa Toprakçý wrote:
> Ok David,
> The temperature is what I want. According to my understanding the
> update algorithm corrects the VCM and prevents accumulation of kinetic
> energy in the center of mass. When I checked the com xvg file this is
> clearly seen. Just like the temperature, the com koordinates does not
> change much.
> so it seems the code does not sample such kind of motion efficiently.
> Such a simulation may be sampled under external forces but that would
> be too unrealistic. Because it would be better to sample under intermolecular forces.
Actually I think the COM motion is subtracted only when you have
external forces, or when you specify COM groups. Usually one has just
COM removal for the whole system, but you have turned off even that
So the conclusion is that if the ligand sticks to the protein, there are
large force holding it there.
Dr. David van der Spoel, Dept. of Cell & Mol. Biology
Husargatan 3, Box 596, 75124 Uppsala, Sweden
phone: 46 18 471 4205 fax: 46 18 511 755
spoel at xray.bmc.uu.se spoel at gromacs.org http://xray.bmc.uu.se/~spoel
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