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

Shima Arasteh shima_arasteh2001 at yahoo.com
Fri Jun 15 10:27:23 CEST 2012

I read that it doesn't matter if the protein moves and even protrudes the box. It's OK, but there is a question here; why doesn't the box move rather than the protein? 

Is it possible for box to be defined every step?, then the protein would stay in the center of the box.


 From: Mark Abraham <Mark.Abraham at anu.edu.au>
To: Discussion list for GROMACS users <gmx-users at gromacs.org> 
Sent: Thursday, June 14, 2012 12:22 PM
Subject: Re: [gmx-users] protein near the edges of simulation box

On 14/06/2012 5:47 PM, Shima Arasteh wrote: 
Dear gmx friends,
>I put a protein in a simulation box filled of water molecules and entered the mdrun command. After the simulation, I found the protein near one of the edges of the box and not in center. What is the problem? Anyone may suggest me? 
>Does it mean that the simulation is meaningless? 
>I expect the protein to stay in the center of box and goes unfold by passing the time.
See http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions


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