From: Axel Kohlmeyer (
Date: Mon Mar 06 2006 - 01:01:20 CST

On Mon, 6 Mar 2006, L. Michel Espinoza-Fonseca wrote:

dear michel,

if you have enough water around your peptide, the following may work:

load the trajectory, then use a hacked version of the fitframes
script, that does only move the selection, and apply pbc.

depending on your trajectory format (some do store the box information,
some not), you have to set the box dimensions as well (see set_unitcell)
and then apply pbc based on the thusly stored info (i have used a hacked
version of pbcwrap for that, attached). so that in the end you you
something like:

source set_unitcell.tcl
source pbcwrap.tcl
mol new waitfor all
set_unitcell 11.0 11.0 11.0
animate goto 0

and then do your analysis.

good luck,

MEF> Dear all,
MEF> I've been trying to analyze the contacts between water and a given
MEF> peptide from my trajectories. I used a nice script provided by one of
MEF> the VMD users. Everything went well, except from the fact that VMD is
MEF> not able to count the water molecules around my peptide from the image
MEF> of my periodic box. I've read some issues related to the pbc and VMD
MEF> (computation of hbonds, for instance), and according to what I read,
MEF> there is not such handling of pbc in VMD. Do you have any suggestions?
MEF> I tried to use some artifacts such as drawing images of the water box,
MEF> but it didn't work.
MEF> Thanks!
MEF> Michel

Axel Kohlmeyer
   Center for Molecular Modeling   --   University of Pennsylvania
Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323
tel: 1-215-898-1582,  fax: 1-215-573-6233,  office-tel: 1-215-898-5425
If you make something idiot-proof, the universe creates a better idiot.