[gmx-users] editconf

Tsjerk Wassenaar tsjerkw at gmail.com
Thu Nov 4 06:48:47 CET 2010

Hi Mustafa,

Check the section on periodic boundary conditions in the manual. Also
be sure to use 'show cell' in Pymol to display the triclinic unit
cell. That will show you the differences. Besides that, do a direct
comparison of the lines encoding the boxes; either the last line of a
.gro fil, or the line starting with 'CRYST1' in a.pdb file.



On Thu, Nov 4, 2010 at 1:23 AM, mustafa bilsel <mfbilsel at gmail.com> wrote:
> Hi,
> when I  choose different box types and draw them by Pymol, I see no visual
> difference between them. At least cubic must be different from the others.
> What is the reason for this?
> best wishes
> --
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Tsjerk A. Wassenaar, Ph.D.

post-doctoral researcher
Molecular Dynamics Group
* Groningen Institute for Biomolecular Research and Biotechnology
* Zernike Institute for Advanced Materials
University of Groningen
The Netherlands

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