From: Diship Srivastava (dishipsrivastava_at_gmail.com)
Date: Thu Oct 07 2021 - 08:07:53 CDT
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 <premabasaknanda_at_gmail.com>
> 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
> Please help.
-- Diship Srivastava JRF Department of Chemistry IIT(ISM) - Dhanbad India
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