[gmx-users] angular COM removal
David van der Spoel
spoel at xray.bmc.uu.se
Sat May 9 12:47:02 CEST 2009
XAvier Periole wrote:
> I am asking for the angular removal of the COM motion of a protein assembly
> in gromacs-4.0.4.
> - grompp gives a strange warning:
> checking input for internal consistency...
> WARNING 3 [file md.mdp, line unknown]:
> Removing the rotation around the center of mass in a periodic system
> (this is not a problem when you have only one molecule).
> - the lines are:
> nstcomm = 1
> comm-mode = angular
> comm-grps = protein
> Then the nstcomm and comm-mode appear to be correctly defined in the tpr
> generated. However during the run the angular removal of the COM is
> clearly not
> done. The protein assembly is rotating ...
> Any reason for this?
Is this in parallel with DD?
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David van der Spoel, Ph.D., Professor of Biology
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
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