On May 9, 2009, at 12:47 PM, David van der Spoel wrote:
XAvier Periole wrote:
Dears,
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 file
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?
Yes, indeed. But according to Berk's earlier comments on a related
problem this
should be fine.
Note that the warning concerning the use of angular COM removal and DD
did not
appear in grompp.
XAvier.
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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.
sp...@xray.bmc.uu.se sp...@gromacs.org http://folding.bmc.uu.se
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