[gmx-users] comprehension of comm_grps

Christian Seifert cseifert at bph.ruhr-uni-bochum.de
Tue Sep 16 09:35:31 CEST 2008

Dear GMXer,

I have a protein which is stretched in one dimension and therefore use a
rectangular box (filled with water/ions). To protect the protein from
self interactions over the pbc, the protein may not rotate in this
rectangular box.

The nearest solution would be to set:
comm_mode = angular
comm_grps = system

But (according to previous threads in this list) this would lead to
clashes at the pbc boundary.

Another idea would be the following setting:
comm_mode = angular
comm_grps = protein

But I don't this would lead to one of the following two problems:
A) "comm_grps = protein" just change the position of the calculated
center of mass from the whole system to the position of the center of
mass of the protein and still rotates the WHOLE SYSTEM, which would lead
to the same problem described above or
B) "comm_grps = protein" deletes just the rotation of the PROTEIN around
the center of mass of the protein, which would lead to small shear
forces at the surface of the protein with the water (which might perhaps
be neglected).

Which problem (A or B) occurs? Are there other solutions?

Best wishes,

M. Sc. Christian Seifert
Department of Biophysics
University of Bochum
ND 04/67
44780 Bochum
Tel: +49 (0)234 32 28363
Fax: +49 (0)234 32 14626
E-Mail: cseifert at bph.rub.de
Web: http://www.bph.rub.de

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