[gmx-users] angular COM removal
x.periole at rug.nl
Sat May 9 12:55:14 CEST 2009
On May 9, 2009, at 12:50 PM, David van der Spoel wrote:
> David van der Spoel wrote:
>> XAvier Periole wrote:
>>> I am asking for the angular removal of the COM motion of a protein
>>> 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
>>> (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
Agreed. But the phenomenon I observe is not affected (it happens with
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?
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> David van der Spoel, Ph.D., Professor of Biology
> Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala
> 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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