From: PREMANANDA BASAK (premabasaknanda_at_gmail.com)
Date: Thu Oct 07 2021 - 07:10:34 CDT
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.
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