[gmx-users] comm-grps

Erik Lindahl lindahl at stanford.edu
Fri Oct 11 04:09:59 CEST 2002

Bert de Groot wrote:

>Hi all,
>I've got a question concerning com-grps. There are two groups
>in my system of which I would like to keep the center of mass
>translation to zero. So I've defined those groups (plus a rest
>group) in make_ndx, and hoped that the following .mdp setup
>should do the job:
>; mode for center of mass motion removal = 
>comm-mode                = Linear
>; number of steps for center of mass motion removal = 
>nstcomm                  = 1
>; group(s) for center of mass motion removal = 
>comm-grps                = around_1695 around_907 others
>In the simulation, however, I see a significant c.o.m. motion
>of all of the groups, that seems to be exactly coupled
>with the deformation of the box size (which is quite large, 
>on purpose). Is there a way to freeze the c.o.m. motion in an 
>absolute sense (so irrespective of any changes in the box dimensions)?
Hi Bert,

This might have to do with the way we scale the coordinates when the box 
is changed
in Berendsen pressure coupling. Do you see it with Parrinello-Rahman 
coupling too?



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