[gmx-users] protein near the edges of simulation box

Shima Arasteh shima_arasteh2001 at yahoo.com
Fri Jun 15 17:26:18 CEST 2012



 From: Elton Carvalho <eltonfc at if.usp.br>
To: Discussion list for GROMACS users <gmx-users at gromacs.org> 
Sent: Friday, June 15, 2012 7:43 PM
Subject: Re: [gmx-users] protein near the edges of simulation box
On Fri, Jun 15, 2012 at 1:23 PM, Tsjerk Wassenaar <tsjerkw at gmail.com> wrote:
> You can specify the protein to have no net center of mass
> motion, by setting it as comm_grps in the .mdp file.

If the user is just concerned about visualization, trjconv -center
solves his problem.

Elton Carvalho
Tel.: +55 11 3091-6985/6922
Dept Física dos Materiais e Mecânica
Instituto de Física
Universidade de São Paulo
P.O. Box 66318 - 05314-970 São Paulo-SP, Brazil
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