From: Heshe Peshkin (
Date: Tue Jun 29 2004 - 14:58:01 CDT


I have the following problem: I am trying to make an "inbox" (wrapped)
movie of a polymer system with periodic boundaries. Contrary to the
unwrapped version, where I only have one PSF file for all the steps and
all the frames can be incorporated into one unit, here each step has its
own PSF (connectivity) and PDB (coordinates) file and each frame behaves
as separate. It is important that I make the movie exactly in the wrapped
version because there are some association going on in the system and I
might not capture all of it if I am looking at the unwrapped version (for
example if two elements are exactly one box away i will see them as
separate but in fact they will be associated).
Working with dynamic bonds doesn't help because it creates artificial
bonds between neighboring but not connected atoms, and between the
associating elements as well (or if the cutoff distance is too big then a
part of the existing bonds disappears). And last but not least, loading
all the frames, opening them one by one and rendering snapshots will take
So - how can I make my movie?

Thanks in advance for any ideas.

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