[gmx-users] A periodic boundary trajectory with lots of objects: how to get rid of artefacts?

Florian Dommert dommert at icp.uni-stuttgart.de
Tue Nov 23 17:07:33 CET 2010

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On 11/23/2010 04:48 PM, ms wrote:
> Dear GROMACS users,
> I am trying to visualize a trajectory with hundreds of peptides which
> come and go out and in the faces of the periodic box. Problem is, when
> they cross the periodic boundary, the visualization software (I tried
> both VMD and PyMol) create visual artefacts by visualizing nonsensically
> long bonds crossing the box -which I understand, since the algorithms
> seem to have no clear notion of PBC.
> Using -pbc nojump or similar, given my experience with identical systems
> only containing less peptides, is not going to work (peptides are going
> to be "broken").

So I think a trjconv with the option -pbc whole will give a trajectory
that gives nice visualization of unbroken peptides


> Since all I want is some nice snasphot of the trajectory to show and not
> analysis, I feel that a much easier solution would be to find a setting
> in the visualization softwares that simply do not visualize bonds longer
> than a threshold. However I can't find such a setting. Does one exist?
> Does a "PBC mode" exist? What kind of solution do you propose? I googled
> quite a bit but I couldn't find much.
> Thanks,
> Massimo

- -- 
Florian Dommert

Institute for Computational Physics

University Stuttgart

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70569 Stuttgart

Phone: +49(0)711/685-6-3613
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