Re: Query about post-process of DCD

From: Diship Srivastava (
Date: Thu Oct 07 2021 - 08:07:53 CDT

Use -
pbc unwrap -all
pbc wrap -compound fragment -center com -centersel "not water and not ion"
animate write dcd wrapped.dcd

On Thu, 7 Oct 2021 at 17:43, PREMANANDA BASAK <>

> I have run MD simulation on a fibril structure consisting of ten monomers
> in a tetragonal box using PBC in NAMD. When I visualize the DCD using VMD,
> I see that one or fewer monomers are jumping on the opposite side of the
> box. I believe that this is an issue of the PBC and which automatically
> puts the images in the central box if any monomer is out of the central box
> from any side. I wish to know the command to post-process the DCDs to reset
> the entire fibril into its original assembly, i.e. reversing the process of
> re-centering.
> Please help.

Diship Srivastava
Department of Chemistry
IIT(ISM) - Dhanbad

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