[gmx-users] remove periodic boundary in tpr file

Tsjerk Wassenaar tsjerkw at gmail.com
Thu Oct 4 10:16:06 CEST 2007

Hi Jaowei Tang,

Better use a .pdb or .gro file. Maybe the starting structure (obtained after
running pdb2gmx)?
By the way, if you removed the jumps over the boundary (you don't really
want to remove periodicity :p) you must already have a proper structure. Or
you can then extract the first frame from the trajectory and use that as the
starting point.


On 10/4/07, tangxuan <tangxuan82 at gmail.com> wrote:
> Dear all,
> I am try to use g_rms to a protein, but its start structure in the
> simulation is not in one box. I removed the periodicity for the xtc file
> by trjconv, but do not know how to remove the periodicity in the tpr
> file. Could you give me some suggestions?
> Thank you.
> Jiaowei Tang
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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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