VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_cmm.chem.upenn.edu)
Date: Fri May 25 2007 - 11:00:48 CDT

On Fri, 25 May 2007, Lechuga, Javier wrote:

javier,

JL> Hello,
JL>
JL> In order to get the coordinates of the atoms of one frame in a
JL> Molecular Dynamics simulation, I am using the script attached.
JL>
JL> It seems to work fine, however, when I have periodic boundary
JL> conditions, I am getting the coordinate values of the periodic atom.
JL> Therefore, when I represent those values, I see the atoms jumping
JL> from one side to the other.

you are getting whatever your MD program outputs. VMD does not
change anything by itself upon loading coordinates and apart
from the representations, none of the VMD functionality as
such is PBC aware.

if you want to modify coordinates of atoms with respect to
PBC (wrapping/unfolding), you can try out the PBCtools plugin
(type 'pbc' on the vmd commandline to get a command summary).

cheers,
   axel.

JL>
JL> I wonder if there is a way to obtain the global coordinate values of the atoms.
JL>
JL> Thank you
JL> 

-- 
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Axel Kohlmeyer   akohlmey_at_cmm.chem.upenn.edu   http://www.cmm.upenn.edu
   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
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