VMD-L Mailing List

From: Ducasse Laurent (l.ducasse_at_ism.u-bordeaux1.fr)
Date: Mon Mar 30 2015 - 09:00:31 CDT

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

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Dr Ducasse Laurent
Institut des Sciences Moléculaires
UMR 5255 CNRS
Groupe THEO
Université de Bordeaux
F-33405 Talence cedex
laurent.ducasse_at_u-bordeaux.fr
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