VMD-L Mailing List

From: Thomas Evangelidis (te8624_at_mbg.duth.gr)
Date: Tue Nov 20 2007 - 18:09:26 CST

Oliver,
are you interested in reducing the size of your trajectories by deleting every
atom that is longer than a cuttof distance (you can define this) from your
macromolecule/s. In this way you can make them more "handy". I have written a
tcl script that does this job automatically, if you're interested let me know
and I'll send it to you.
regards,
Thomas

>
> 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
>