From: Z. Erge Akbas (
Date: Sun Apr 24 2016 - 14:30:29 CDT

Hi All,

I have a 100 ns MD trajectory composed of two chains of a protein structure
(no ligand). At the initial steps of the trajectory, everything seems
alright. Close to the end of the trajectory, my system got apart (one chain
goes to another periodic box).

After loading my psf and dcd trajectory to VMD 1.9.2 and going to the first
frame, I have tried pbc wrap option by typing in TKConsole

            pbc wrap -center com -centersel "chain B" -compound residue -all

since chain B stays in the current box while chain A goes to other box.
With this pbc wrap command I achieved to keep both chains in the same
periodic box. Chains are wrapped together but there occurs streching bonds
across the periodic box.

After pbc wrap, I tried to apply pbc join followed by pbc unwrap with
following selections and again got no desired change (still streched bonds
in the box).

            [pbc join res -ref “name CA”]

            [pbc unwrap]

In another attempt, I have tried different options such as

            pbc wrap -compound fragment -all -center com -centersel
"protein and chain B"

            (chains still stay apart)

followed by

            pbc wrap -all -compound res -center com -centersel protein

to be able to keep bonded atoms together, chains got together but again
there is streched bonds with this pbc wrap options.

So I know that as a first step I should use

            pbc wrap -center com -centersel "chain B" -compound residue -all

but I do not know what to write next for the nonbonded atoms (due to
crossing the boundary of the periodic box) to disappear and to have a
smooth trajectory.

Any help would be appreciated, thanks in advance.

*Zeynep Erge AKBAS*
*Bogazici University, Polymer Research Center*