[gmx-users] angular COM removal

[David van der Spoel]

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?


> 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.
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se