[gmx-users] comm-grps

[Bert de Groot]

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)?

cheers,

Bert

____________________________________________________________________________
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
http://www.mpibpc.gwdg.de/abteilungen/071/bgroot
____________________________________________________________________________