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.
Thanks,
Massimo
--
Massimo Sandal, Ph.D.
http://devicerandom.org
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