[gmx-users] Physical problems of comm removal

Christian Seifert cseifert at bph.ruhr-uni-bochum.de
Thu Feb 12 16:00:30 CET 2009

Hi users!

I simulate a stretched protein in TIP4P water in a cubic box
(6.83x9.60x13.58=890) with pbc. During a 50 ns simulation, my protein
must not rotate (otherwise, it will interact with itself). I found three
possibilities to avoid a self interaction: (1) a bigger box, (2)
restraints or (3) comm removal.

In details:
(1) bigger box:
I need at least a diameter of 13.58 nm in every direction to avoid a
self interaction (because of a possible rotation of the protein). For a
cubic box, this would be (13.58^3 =) 2504 nm^3. For a truncated
octahedron still 1928 nm^3, which would still be twice the box size I
use now. This is not suitable for me.

(2) restraints:
These are "long-time" runs, where I want to observe domain movement, so
restraints are not an alternative for my simulation.

(3) comm removal:
To use my stretched box, I have to use COMM-MODE = Angular. This mode
provokes artifacts, if I use it only on my protein and is therefore
forbidden since GMX4.0.3. But what happens, if I use it for my whole
system? My protein has a mass of 142800 a.m.u. and the solvent has a
mass of 998100 a.m.u. Let us assume, that the solvent movement reduces
itself, because its movement is undirected and the mass of the protein
is high enough to fall into account (which might not be true because:

v_{comm_removal}= 1 / (m_{solvent} + m_{protein}) \cdot
\sum_{i(solvent)}^n{(solvent)} ( m_i \cdot v_i) \cdot
\sum_{j(protein)}^o{(protein)} ( m_j \cdot v_j)

with \sum v_i=0 (because the movement of the solvent is undirected) the
equation would be:

v_{comm_removal}= 1 / (m_{solvent} + m_{protein}) \cdot 
\sum_{j(protein)}^o{(protein)} ( m_j \cdot v_j)

which weights the movement of the protein with its mass, put divides it
by the mass of protein+mass, what may result in a to small removal of
the comm.)

Beside this problem, do I have to expect that there might be other
problems with COMM-MODE = Angular, COMM-GRPS = System and a cubic box
with pbc?

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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