[gmx-users] comm-grps

Bert de Groot bgroot at gwdg.de
Thu Oct 10 10:37:09 CEST 2002

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)?



Dr. Bert de Groot

Max Planck Institute for Biophysical Chemistry
Theoretical molecular biophysics group
Am Fassberg 11 
37077 Goettingen, Germany

tel: +49-551-2011306, fax: +49-551-2011089

email: bgroot at gwdg.de

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