[gmx-users] box dimension

Nilesh Dhumal ndhumal at andrew.cmu.edu
Mon Oct 17 22:05:46 CEST 2011


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?

I am using Gromacs 4.0.7 version.



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