Re: Annealing process of silica with excluded block

From: Jeff Comer (
Date: Mon Sep 15 2014 - 09:30:57 CDT

Hello Marzieh,

"wrapAll" does not affect the physics of the system (except sometimes
for a few specialized NAMD features). When the Si and O atoms "pass
through the boundaries of the system", they only appear to do so. I
would suggest reading more about how periodic boundary conditions

Best wishes,

Jeffrey Comer, PhD
Assistant Professor
Department of Anatomy and Physiology
College of Veterinary Medicine
Kansas State University

On Fri, Sep 12, 2014 at 10:22 AM, Marzieh Alishahi
<> wrote:
> Dear NAMD users,
> I want to perform “Annealing” process on a silica (Silicon Dioxide) solid
> material which was primarily created by Inorganic Builder toolbox on VMD and
> the point is that the silica is a cube with a smaller cube cut out from the
> upper corner. That means at the upper surface of silica, there is a part of
> excluded volume, so I cannot use “wrapAll on” in my NAMD configuration file.
> And if I turn off the “wrapAll” command, the silica molecules will pass the
> boundaries during annealing process. I Also try adding restrain on silica
> atoms, but it seems somehow meaningless since it will cancel all the
> movements of atoms during annealing. I would be so grateful if any one could
> help me to solve this problem.
> Thanks in advance,
> Marzieh

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