VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_cmm.chem.upenn.edu)
Date: Thu Oct 09 2008 - 14:14:57 CDT

On Thu, 9 Oct 2008, mahesh naalla wrote:

MN> Hello everyone,
MN>
MN> How can I draw density distribution plots using HISTORY file from DL_POLY
MN> (MD simulations).

those are two independent issues:

1) how to load DL_POLY trajectories.

VMD should support loading this file format.
once you have read a trajectory into VMD it
does not matter in which format it was originally
stored.

2) how to compute/plot density distributions.

that depends entirely on what _kind_ of density
distribution you are interested in and how you
want to "plot" it. VMD provides the volmap plugin
that allows computing different kind of density
distributions on a 3 dimensional grid and then
either store them in .dx format or load them into
VMD as volumetric data sets which can then be visualized
in the usual way (iso-surface, volume slice).

cheers,
   axel.

MN>
MN> Thanks
MN> Mahesh Naalla
MN> 

-- 
=======================================================================
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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If you make something idiot-proof, the universe creates a better idiot.