From: Nima Nouri (
Date: Mon Aug 22 2011 - 18:56:25 CDT

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"

for joining the different parts of a molecule to the C atoms inside the
Periodic Box.

> Thanks for your help,
> Casey


Ph.D Student
Department of Mechanical Engineering
Isfahan University of Technology
Isfahan, Iran