From: Axel Kohlmeyer (
Date: Fri May 16 2008 - 14:46:11 CDT

On Fri, 16 May 2008, Alberto Sergio Garay wrote:



ASG> I am using VMD to calculate a cylindrical density around a particular
ASG> molecule in a lipid bilayer model. I have 10 ns gromacs trajectory (20.000
ASG> frames) to study. My script is not so complicated to take so long time to
ASG> finish its task. Is it OK that the hard disk increases its work as the
ASG> number of frames increases?. Sometimes the PC hang up. I am working in a

that looks like your skipt has a memory leak.
are you by any chance using atom selections and
not deleting them? have you monitored the memory
use during the script.

there also is the bigdcd script (check out the improved version
that i sent out recently that supports non-dcd formats) that
processes data one frame at a time and then deletes it.

ASG> Intel core2duo PC, with 2 Gb of RAM memory under Fedora core 6 linux OS.
ASG> Is there any web site where I can take some pieces of advice to improve my
ASG> tcl/tk scripting?

there are some links and advice on the vmd home page (i forgot where,
you may have to dig a little). for starters you could just have
people here review your script.

other than that, please keep in mind that you can only get
vague advice on a vague description. the more details you
provide the more precise advice people can give you.


ASG> Thank you in advance

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.