VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Tue Nov 20 2007 - 14:41:35 CST

Oliver,
  Please see the "BigDCD" plugin in the VMD script library, or that
has been posted to the VMD-L last a few times in the last few weeks.
Let us know if you have questions.

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Tue, Nov 20, 2007 at 03:28:45PM -0500, Oliver Beckstein wrote:
> Hi,
>
> is there a way to analyse trajectories that are bigger than the
> available RAM? For instance, I have trajectories > 5GiB in size that I
> would like to analyze with VolMap but they can't be loaded because VMD
> insists on keeping the whole trajectory in memory.
>
> A cumbersome work-around would be to split the trajectory into smaller
> chunks, run volmap on each chunk, then average the resulting dx files.
> However, I can think of situations when a simple average is not enough
> (for instance for time correlation functions) and it would very
> convenient if one could just have a (python-style) iterator over a
> trajectory (similar to the 'for timestep in universe.dcd: ....' idiom
> in http://code.google.com/p/mdanalysis/ ).
>
> (Note: I don't think that increasing swap space is a solution because
> that leads to the computer almost grinding to halt when the trajectory
> is loaded.)
>
> Thanks,
> Oliver
>
> --
> Oliver Beckstein * orbeckst_at_jhmi.edu
>
> Johns Hopkins University, School of Medicine
> Dept. of Physiology, Biophysics 206
> 725 N. Wolfe St
> Baltimore, MD 21205, USA
>
> Tel.: +1 (410) 614-4435 

-- 
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
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