[gmx-users] Problem with removing COM translation

Alexandre Suman de Araujo asaraujo at if.sc.usp.br
Thu Aug 12 16:25:03 CEST 2010

Hi Gmxers

I'm simulating a system composed by a protein centered in a sphere of 
water in vacuum.

The water molecules are kept within a virtual sphere with position 
restrains between oxygen atom and a dummy atom fixed at the center of 
the sphere. The protein can move without any restriction.

To prevent the separation between protein and the water globule, I 
defined "comm_grps = Protein Non-Protein" in my .mdp file (I've also 
used the same groups in temperature coupling as suggested in GMX 
manual). However, when I run the simulation the protein COM moves away 
from the center (where it is in the beginning of the simulation) of the 
water sphere. The movement of COM of the water sphere is small (less 
than 1 angstron). For simulations of 5ns this translation is about 2 
angstrons and for a 14 ns simulation it is more than 10 angstrons.

Does anyone could help me with this issue?

As far as I know, the remove of COM motion is made by subtracting the 
COM velocity from the velocity of the atoms within the groups defined in 
comm_grps. Is it possible to really "freeze" the movement of the COM of 
some groups in GROMACS to achieve an absolute static COM?


Alexandre Suman de Araujo                                    *
Faculdade de Ciências Farmacêuticas de Ribeirão Preto        *
Universidade de São Paulo                                    *
Dep. de Física e Química                                     *
Grupo de Física Biológica     * e-mail: asaraujo at fcfrp.usp.br*
Av. do Café, s/n°             * e-mail: ale.suman at gmail.com  *
CEP: 14040-903                * Phone: +55 (16) 3602-4172    *
Ribeirão Preto, SP, Brasil    * Phone: +55 (16) 3602-4222    *

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