[gmx-users] box dimension
Mark.Abraham at anu.edu.au
Tue Oct 18 00:36:02 CEST 2011
On 18/10/2011 7:05 AM, Nilesh Dhumal wrote:
> 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.
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