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

[Mark Abraham]

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

Mark
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