VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Tue Aug 23 2011 - 09:26:09 CDT

On Mon, Aug 22, 2011 at 6:54 PM, Casey Johnson
<j.casey.johnson_at_gmail.com> wrote:
> Hello Users,

hello casey,

> 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?

yes. you first have to unwrap the trajectory (this is by the way easiest
done right inside of lammps using dump_modify <dumpid> unwrap yes)
and then wrap the trajectory with pbcwrap again using the -compound fragment
flag. that will preserve all "fragments" (= molecules). the default is wrapping
per atom which will result in the unpleasant bonds across the cell display.

hope that helps,
     axel.

> Thanks for your help,
> Casey 

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