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

ms devicerandom at gmail.com
Tue Nov 23 19:04:57 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.

Cool, thanks! I'll dig it.
I'd really hope there is a pymol option as well, I'll see :)

> 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.

Yep, but if they appear broken because they are at the pbc boundaries is 
no big deal. The problem (and with this I answer also Florian Dommert) 
is that using -pbc tends to "break" stuff *inside* the box.


Massimo Sandal, Ph.D.

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