From: John Stone (
Date: Mon Mar 30 2015 - 17:32:16 CDT

  If you take a close look at the documentation for the pbctools plugin,
you should be able to deal with wrapping over all frames in a single pass with
the "-all" flag if I recall correctly. If your problem is more complex than
that, you can of course use for loops in your own script to get it done if
for some reason the built in functionality in pbctools doesn't quite do what
you have in mind.

  John Stone

On Mon, Mar 30, 2015 at 04:00:31PM +0200, Ducasse Laurent wrote:
> Hi,
> I performed a dynamics for a unit cell containing a cluster of molecules
> using namd and I load a dcd file together with the corresponding psf one.
> Along the dynamics, for particular frames, some atoms of the cluster move
> away from the unit cell. Thus, if I want to save coordinates into a pdb
> file for every frame, for these "wrong" frames, the pdb coordinates will
> be wrong (some atoms are far away from each other).
> I only can rebuild the correct cluster using pbc wrap for one frame
> How can I manage the dcd file (pbc wrap/unwrap ?) to tackle this problem ?
> Best regards
> Laurent
> ***************************
> Dr Ducasse Laurent
> Institut des Sciences Moléculaires
> UMR 5255 CNRS
> Groupe THEO
> Université de Bordeaux
> F-33405 Talence cedex
> [1]
> ****************************
> References
> Visible links
> 1.

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