AW: pbc error

From: Norman Geist (
Date: Mon Sep 02 2013 - 01:44:18 CDT

If you have more than only the pentamer in your cell, "-centersel all" will
NOT do anything. Try to select you pentamer only for the centering maybe
"-centersel protein" or similar. The effects you see are just normal and
they must occur if parts of you molecule cross the bounds of a periodic box.
If the problem persists, your box might simply be too small. You should do
some deeper thinking how pbc actually works to understand and predict the
behavior you see.

Norman Geist.

> -----Ursprngliche Nachricht-----
> Von: [] Im
> Auftrag von jinxj
> Gesendet: Montag, 2. September 2013 04:39
> An: namd
> Betreff: namd-l: pbc error
> Dear professor:
> We simulated a pentamer protein with NAMD. I am confused about that
> some part of the pemtamer fluctuated in and out of the box when I
> viewed the trajectory in VMD. Then I dealed with pbctools in vmd and
> failed. The command used are at below.
> package require pbctools
> pbc wrap -all -compound res -center com -centersel all
> After this operation, all parts of the protein was centered. But
> there are errors in some of the structures. When I viewed the treated
> trajectory in VMD, the unrecognizable structure coordinates were
> generated.
> What can I do about this problem?
> Xiaojie

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