On Wed, 26 Dec 2007 09:01:22 +0100
David van der Spoel <[EMAIL PROTECTED]> wrote:
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".
I do not think you want to remove the center of mass motion of your
peptide, and certainly not of your solvent. The diffusion of the peptide
is certainly something you should expect. If it looks like a flying
ice cube that means that there are some parameters that you should
modify in your mdp file.
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.
[EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se
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NMR & Molecular Dynamics Group
University of Groningen
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