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

[Tsjerk Wassenaar]

http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions

Cheers,

Tsjerk

On Thu, Jun 14, 2012 at 10:26 AM, Shima Arasteh
<shima_arasteh2001 at yahoo.com> 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.
>
> Thanks in advance
> Sincerely,
> Shima
>
>
>
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-- 
Tsjerk A. Wassenaar, Ph.D.

post-doctoral researcher
Molecular Dynamics Group
* Groningen Institute for Biomolecular Research and Biotechnology
* Zernike Institute for Advanced Materials
University of Groningen
The Netherlands