VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Thu Aug 04 2011 - 13:44:33 CDT

On Tue, Aug 2, 2011 at 8:51 PM, Vivek Ranjan <vranjan_at_ncsu.edu> wrote:
> Hello,
> I generated a dcd file using LAMMPS with a periodic boundary condition.
> First I load a psf file in vmd and then read in dcd file. In the dynamics,
> whenever an atom crosses the box boundary, a long line is created.
> Eventually, there are too many such lines and it is difficult to view the
> actual molecules inside. Is there a way I can get rid of these lines and
> view only atoms ?

just use a VDW representation. it only shows atoms and no bonds.

the "long line" is due to a bond being defined and one of the two atoms
of the bond being moved across a periodic boundary.

if you _do_ want to keep the bonds, then you have two options:
1) tell LAMMPS to "unwrap" your trajectory before it is written out
(by using: dump_modify <dumpid> unwrap yes)
2) use the pbctools plugin to unwrap the trajectory after the fact.

cheers,
     axel.

> Please let me know.
> Thank you,
> Vivek 

-- 
Dr. Axel Kohlmeyer
akohlmey_at_gmail.com  http://goo.gl/1wk0
Institute for Computational Molecular Science
Temple University, Philadelphia PA, USA.