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).
In addition, this is not a strange warning, because this may introduce
artifacts. In particular when you have water as well, you are basically
violating Newton's second law (Fji = -Fij). One could argue that grompp
should look into whether you have one molecule or not.
- 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?
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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