[gmx-users] center of mass removal

David van der Spoel spoel at xray.bmc.uu.se
Wed Dec 26 09:01:22 CET 2007

Li Qiang wrote:
> hi Christian,
> Thanks for the reply. I have plotted the the rate of center of mass
> motion and found there are peaks with certain time interval. I think
> that is not only a visual problem but like fly ice cube problem(not
> sure). As a comparison, when a large protein is simulated, the
> rate(velocity) of COM is "constant".
> Yes. the default way GROMACS do is system COM removal at each step. 
> how does the program remove this center of mass motion?
By summing the COM momentum and subtracting it from all atoms.

David van der Spoel, Ph.D.
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205. Fax: +4618511755.
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se

More information about the gromacs.org_gmx-users mailing list