From: Axel Kohlmeyer (
Date: Tue Aug 23 2011 - 09:27:20 CDT

On Mon, Aug 22, 2011 at 7:56 PM, Nima Nouri <> wrote:
> on Tue, Aug 23, 2011 at 3:24 AM, Casey Johnson <>
> wrote:
>> Hello Users,
>> I am using the Lammps dump command to dump a .dcd file. I load a .pdb
>> into VMD then load the .dcd info into that file, I then try to wrap/unwrap
>> the bonds so they are in one unit cell, however, when I wrap/unwrap the
>> file, the molecules end up way outside the unit cell. I know this is
>> because it's positioning the atoms how they would be in the periodic
>> boundaries but I would like to see how the molecules are actually packing in
>> the cell. Is it possible to wrap/unwrap the bonds so they stay in the given
>> unit cell dimensions?
> if I got you correctly you can try the join command.
> you can find the documentation in the vmd website on the pbctools plugin.
> it should be sth like :
> pbctools join res -ref "name C"

all pbctools commands are prefixed with "pbc", but
generally, you want to avoid pbc join as much as possible,
since it is the by far most expensive operation.


> for joining the different parts of a molecule to the C atoms inside the
> Periodic Box.
>> Thanks for your help,
>> Casey
> cheers
> N.Nouri
> Ph.D Student
> Department of Mechanical Engineering
> Isfahan University of Technology
> Isfahan, Iran

Dr. Axel Kohlmeyer
Institute for Computational Molecular Science
Temple University, Philadelphia PA, USA.