[gmx-users] C.O.M problem

Shavkat Mamatkulov shavkat at theorie.physik.uni-muenchen.de
Mon Jun 30 23:32:01 CEST 2003

Dear gromacs users,

I am doing simulation on a water slab placed in vacuum and wont to see how
fluctuates center of mass the water slab on time. my initial box was cubic
(3,3,3) - geometrical center was 1.5, 1.5, 1.5.

i have shifted my slab to the new center 1.5, 1.5, 3 by
editconf along Z direction and set box sizes as x=3,y=3,z=6, so i get a
rectangular box with  vacuum in two side of  the water slab. i have
termalized my system for 200 ps with
comm-mode = Linear

then i set
comm-mode = None
expecting to see the center of mass
fluctuation, but after  1 ns simulation in NVT ensemble, my system always
going back to origin, i.e. from geometrical center 1.5, 1.5, 3 to 1.5, 1.5, 1.5.

Can anyone met this problem? what i have to do to keep of slab in new
Thank you in advance

Dr. Shavkat Mamatkulov
Sektion Physik,
LMU Theresienstr. 37, 80333
Tel: 49-89-2180 4596
Fax: 49-89-2180 4517
shavkat at theorie.physik.uni-muenchen.de

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