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

ms devicerandom at gmail.com
Tue Nov 23 16:48:56 CET 2010

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").

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.


Massimo Sandal, Ph.D.

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