[gmx-users] angular COM removal

XAvier Periole x.periole at rug.nl
Sat May 9 12:41:30 CEST 2009


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?


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