From: Axel Kohlmeyer (
Date: Wed Mar 05 2008 - 12:37:02 CST

On Wed, 5 Mar 2008, Michael Kreim wrote:

MK> Hello,

hello michael,

MK> I am analysing my DCD-trajectories with VMD.
MK> But my scripts are running slow.

perhaps there are ways to improve them. quite
a few examples that were posted here were horribly
inefficient. there are quite a few tricks to make
analysis faster.

MK> Therefore my question: Is it possibly to run VMD in parallel?

not as such. a few operations are multi-threaded, but scripting
is inherently serial. what you can consider is doing the analysis
on parts of your data in parallel with individual copies of VMD
and then combine the results.

MK> I am sitting an on a 2-dual-core-machine and in NAMD I can do something
MK> like:
MK> charmrun namd2.6.linux ++local +p8 ./config.namd
MK> Is it possible to do something similar in VMD?
MK> I am starting my VMD-scripts with vmd -dispdev text -e so there is no
MK> need for the graphic-features.
MK> I only would like to run faster vmd-tcl-analysing-scripts.

if you post your scripts, we may be able to comment
on their inherent effciency.


MK> Thanks a lot and best regards,
MK> Michael

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.