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

ms devicerandom at gmail.com
Tue Nov 23 20:32:35 CET 2010

On 23/11/10 17:00, Mark Abraham wrote:
> If you only want a snapshot, then simply write a single chosen frame to
> a .gro or .pdb using trjconv. Load only that into VMD, and it won't
> generate PBC-crossing bonds.
> If you want a movie, then there I seem to recall that there is a VMD
> option to generate bonds for each frame, and not to use those from the
> first frame. Ask their mailing list. Such bonds will not traverse the
> PBC, obviously. There is no general solution for bonds visualized on a
> single set of coordinates, however - over a trajectory, either molecules
> appear to diffuse out of the box, or appear to break.

For PyMol, here is the solution:

thanks for pointing!

Massimo Sandal, Ph.D.

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