VMD-L Mailing List

From: Olaf Lenz (lenzo_at_mpip-mainz.mpg.de)
Date: Tue Dec 08 2009 - 07:39:39 CST

Hi!

It would help a lot if you could send a snapshot of the system, as it is
pretty hard to imagine what you want to do from your writing. Better
even, send sample files of the system.

Jennifer Williams wrote:
> I am trying to look at a trajectory of my molecule. I have a long alkyl
> chain anchored at one end. The problem arises because this chain crosses
> over the periodic boundary conditions. I am visualizing a 2x2 cell as my
> unit cell is small.

If you need to visualize more than one image, this means that your chain
actually stretches more than a single image? With this I do NOT mean
that the chain has some atoms in one image and some in the other, but
that the chain actually has an extension longer than the box size?

In that case, the pbctools can not help you.
What you could do is to write a script that actually duplicates the
atoms. Then the dynamic bonds can help you to draw the bonds.

Or is that not the problem?

Olaf