[gmx-users] non squares box

Tsjerk Wassenaar tsjerkw at gmail.com
Sun Jun 21 12:42:32 CEST 2009

Hi Omer,

To check your periodicity use genconf:

genconf -f in.pdb -o out.pdb -nbox 2 2 2



On Sun, Jun 21, 2009 at 11:23 AM, Omer Markovitch<omermar at gmail.com> wrote:
> Dear All,
> I would like to ask your help on the following - I want my simulation to
> include a surface, and have PBC.
> The surface I chose is aligned on the XY plane. However, the surface is not
> a square.
> The surface dimensions are a=b=169.2 & c=6.9 Angstroms, the angles are:
> bc=ac=90 & ab=120 degrees.
> I have used "editconf -f -box 16.92 16.92 0.69 -angles 90.0 90.0 120.0". To
> test this, I have used "trjconv -pbc nojump -center yes -boxcenter zero". My
> problem is that the trjconv generates a structure where some of the surface
> atoms are cut and/or overlapping...
> Could you please help me? Wheres the problem?
> The input PDB I use is about 2 MB in size, so it can't be attached here.
> Koby Levy research group,
> Weizmann Institute of Science.
> http://www.weizmann.ac.il/sb/faculty_pages/Levy/
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Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623

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