VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Tue Nov 20 2007 - 16:26:34 CST

One other comment on this since I missed the part of your question
referring to VolMap:
  You can modify the BigDCD script so it processes things in chunks rather
than a single frame at a time. This avoids the issue of having to
pre-dice your trajectory, or having VMD explicitly loop loading chunks
in your own code. You'd still have to make VolMap operate on the chunk
size that fits in physical memory, and then combine the results (you
didn't specify which operations you're doing with VolMap so I don't
know what method of combination would be required).

Cheers,
  John

On Tue, Nov 20, 2007 at 02:41:35PM -0600, John Stone wrote:
>
> 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
> WWW: http://www.ks.uiuc.edu/~johns/ Fax: 217-244-6078 

-- 
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