From: Olaf Lenz (
Date: Fri Aug 28 2009 - 04:06:39 CDT

Hash: SHA1


Sorry for the late reply, I was away on a conference.

Yew Yong Kin wrote:
> order to produce some animation in VDM environment. Thank to you guys
> for the nice work of PBCTools plugin, that make my life much easier, I
> was able to remove the overstretching bond in the course of the
> animation. However, I would like to know is there any way of prescribing
> the linking of the bonds by the owner rather than using the unwrap or
> join functions in PBCTools?

I do not completely understand what you mean by "prescribing the
linking". You can easily get and modify the bonds of an atom in a
simulation via the VMD scripting interface.

The PBCtools do currently not support any such operation. In principle,
it would be easy to write a script that simply removes all overstretched
bonds by checking for any bonds that are longer than half the box size,
but it hasn't been done yet. If you want to do that, please contribute
the code to pbctools, I think it would be a nice addition!

Note, however, that the bond structure throughout a simulation is fixed,
so you can not easily modify the bond structure depending opn the
trajectory frame - if you remove a bond, it is gone for the rest of the
simulation, if you do not explicitly create it again. If you need that,
you would have to somehow connect to the frame update of VMD. Also, this
would most probably causea serious performance problem.

As a suggestion to the VMD developers, I could also think that one could
add a function to the representations trajectory tab that would allow
not to draw any bonds that are longer than a given number. I think that
this would solve most of the problems with overstretched bonds. However,
I do not know how compliated it would be to implement this.


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