[gmx-users] box dimension

[Mark Abraham]

On 18/10/2011 7:05 AM, Nilesh Dhumal wrote:
> Hello,
>
> I have saved the coordinates of snapshot from trajectory in pdb file.
>
> The dimesnion of box in pdb file are
> 32.805   32.805   32.805  90.00  90.00  90.00 P 1
>
> I am trying to find  atoms close to center of box.
>
> there are  atoms whose distance from center is more that ~17 A. My center
> coordinates are 0.0 0.0 0.0.
>
> How is it possible?

Molecules diffuse across periodic boundaries during the simulation. 
While computing interactions, mdrun corrects for periodicity on the fly, 
but does not trouble itself to guess what manner of post-processing you 
would like to do. There is a suggested trjconv workflow on the the 
GROMACS website. I suggest you try it.

Mark