Re: how to fix the problem

From: Jeff Comer (
Date: Fri Nov 14 2014 - 20:02:09 CST


If you don't like where the pbc join put the protein, just shift it
where you would like it by a cell basis vector (using $sel move
$vector). Shifting by a cell basis vector or any linear combination of
cell basis vectors with integer coefficients doesn't change the system

Forgive me if you already understand this, but I should point out that
various pbctools commands only change how the system looks and don't
change it in any physically meaningful way. In general, how you wrap
your structure doesn't matter to NAMD. For example, even if VMD makes
it look like a bond crosses almost the entire system except for 2
angstroms, NAMD considers only the minimum distance between two
periodic images, which is just 2 angstroms apart.

Jeffrey Comer, PhD
Assistant Professor
Institute of Computational Comparative Medicine
Nanotechnology Innovation Center of Kansas State
Kansas State University
Office: P-213 Mosier Hall
Phone: 785-532-6311

On Fri, Nov 14, 2014 at 5:19 PM, Liqun Zhang <> wrote:
> Dear all:
> I have run a simulation for a protein in lipid system for a very long time.
> In order to remove the pbc effect, I unwrapped the trajectory for protein
> and the lipids using pbc commands in vmd program, which made part of the
> protein broken in the z-direction. But when I tried to use join command to
> join the broken part to the major part of the protein, the major part of the
> protein instead was shifted to the broken part. I am not sure how to solve
> the problem. Can I get some suggestion here? Thank you very much.
> Best,

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