[gmx-users] center of mass removal

[David van der Spoel]

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