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

[ms]

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:
http://www.mail-archive.com/pymol-users@lists.sourceforge.net/msg07721.html

thanks for pointing!
m.

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