[gmx-users] Protein out of box
Mark Abraham
Mark.Abraham at anu.edu.au
Wed May 28 09:13:42 CEST 2008
Alif M Latif wrote:
> Dear GROMACS users and developers,
>
> I'm having problem with my protein structure after md simulation. The
> protein structure was outside of the simulation box after the
> simulation. My configuration include my protein structure, DMSO and
> water. After equilibration simulation the protein was still in the
> simulation box. However, after 2 ns of production simulation, only the
> protein structure was out of the simulation box. DMSO and water were
> still in the box.
>
> My question is, is this a sign of something that I did wrong (i believe
> so), or I can just ignore it and try centering the protein again in the
> box. Can anyone please help me out? Comments and suggestions are greatly
> appreciated.
This is a non-problem. Check out
http://wiki.gromacs.org/index.php/Periodic_Boundary_Conditions
Mark
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