VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Mon Sep 24 2012 - 12:47:11 CDT

This is a frequently asked question. The answers are already many times in the mailing list archives. Point one you can tell lammps toWrite unwrapped coordinates. You havento have a properly unwrapped initial configuration any way.

Other than that there is the pbctools plugin that can wrap whole molecules, vmd calls them fragments back into the cell without the bonds to the indesired periodic image


Point two. The pbctools plugin also has multiple options for showing the simulation cell. Since the Information about the box origin is not stored in VMD you may have to tweak that a bit.

Axel
--
Dr. Axel Kohlmeyer akohlmey_at_gmail.com http://goo.gl/1wk0
International Centre for Theoretical Physics, Trieste. Italy.

-----Original Message-----
From: Ivan Moncayo <idmoncay_at_gmail.com>
Sender: owner-vmd-l_at_ks.uiuc.edu
Date: Mon, 24 Sep 2012 11:39:06
To: <vmd-l_at_ks.uiuc.edu>
Subject: vmd-l: Lammps simulation

Hi everyone,

I'm using VMD to visualize a simulation of liquid water with periodic
boundaries. When I see the video using water.psf file the bonds cross the
simulation box due boundaries conditions. My question is whether there is
any way that the bonds do not do this.

An additional question is whether there is a form that appears in the video
lines simulation box defined. I appreciate the care and assistance provided

--
Saludos

Iván Moncayo R.