VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Tue Jul 04 2006 - 22:56:28 CDT

Javad,
  You can probably make this process MUCH faster with various improvements
to your script etc. Most likely your script itself could be written
better, and you may or may not have already discovered that you can make
trajectory loading much faster by using the "waitfor all" option when
loading via text commands, or in the graphical interface. (which prevents
VMD from wasting time updating graphics while it loads...)
If you send your analysis script, I can probably give you a few tips
that will allow it to run much faster.

  John Stone
  vmd_at_ks.uiuc.edu

On Tue, Jul 04, 2006 at 12:14:36PM -0400, Javad Azadi wrote:
> Hi!
>
> I am using VMD to analyze 6ns trajectories produced in gromacs and it is proving to be very slow. I am
> using a MacBook 2.0Ghz base model for this task, but I don't know if it is my system that is to blame. I
> want to measure the distance between two sets of two atoms (distance between atom1-atom2 and the
> distance between atom3-atom4) and the dihedral formed by the atoms (atom1-atom2-atom4-atom3).
> Loading the trajectory takes a while, then going to the label menu and saving the plot also takes a
> while. I can do one trajectory every half-hour with the current method, but is there a faster way using
> VMD?
>
> Thanks,
> Javad Azadi
> Undergraduate Researcher
> The Ohio State University
> jazadi_at_chemistry.osu.edu 

-- 
NIH Resource for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
Email: johns_at_ks.uiuc.edu                 Phone: 217-244-3349
  WWW: http://www.ks.uiuc.edu/~johns/      Fax: 217-244-6078