[gmx-users] angular COM removal
x.periole at rug.nl
Sat May 9 12:50:37 CEST 2009
On May 9, 2009, at 12:47 PM, 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 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
should be fine.
Note that the warning concerning the use of angular COM removal and DD
appear in grompp.
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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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