On May 9, 2009, at 12:50 PM, David van der Spoel wrote:
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.
Agreed. But the phenomenon I observe is not affected (it happens with
both setups
with identical characteristics) and the trick saves a lot of computer
time (amount of solvent)!
- 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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