From: Axel Kohlmeyer (
Date: Wed Jul 25 2007 - 11:04:02 CDT

On Wed, 25 Jul 2007, Rachel wrote:

R> Dear all,

dear rachel,

R> I have VMD installed on IBM cluster, and I need to run some scripts with VMD
R> which takes long time to finish when ran interactively, therefore I am
R> wondering if I submit to queueing system it may be much faster, here is the
R> script I used to submit the job:

that would make rather little sense, because VMD is not 'proper'
parallel program. it has some multi-threading in some commands,
but that is it.


R> #@ job_name = model_VMD
R> #
R> #@ job_type = parallel
R> #@ cpus = 16
R> #@ node_usage = not_shared

16 cpus is probably not giving you much of a speedup, if any,
for most of the regular script code there is no gain at all
(the tcl interpreter is single-threaded).


R> vmd mol new model.prmtop
R> vmd mol addfile model_md1to5.mdcrd type crdbox waitfor all
R> vmd source myscript.tcl
R> vmd myscript

this cannot work either. please check the documentation. to
run VMD in batch script mode you best put _all_ VMD commands into
a single script batch_exe.tcl and then run:

vmd -dispdev text -eofexit -e batch_exe.tcl

however, the best chance to see some speedup would be to
profile your script and optimize the tcl code in it.
_most_ of the commonly used tcl scripts have a significant
potential for speedup (either through a smarter algorithm
or better tcl coding). check out, e.g.:

R> I haven't used VMD in this way before, therefore not sure whether it is the
R> right way to do so. What I really need is a way to use VMD for analysis that
R> takes long time that I can logoff without killing the process.

the 'vmd -eofexit -dispdev text -e script.tcl' thing also works on
a local/interactive machine. just put a 'nohup' in front of it and
add an '&' at the end of the command, so that it is sent into the
background and not terminated when you log off.

R> Thank you in advance for any advice.
R> Kind regards,
R> Rachel


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.