[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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