VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Tue Aug 22 2006 - 21:48:24 CDT

Michel,

On Tue, Aug 22, 2006 at 09:18:06PM -0500, L. Michel Espinoza-Fonseca wrote:
> Hi John,
>
> Thanks for helping me with this. I've done what you suggested and yes,
> when I load both psf and pdb files into VMD, they almost used most of
> the RAM I have available. I did it only running VMD with no graphical
> interface and no other program that can use that memory.

I loaded up the structure and looked at it in the "points" representation
for speed, and colored it by position, index, and a few other things.
Very cool :-)

> It if fine
> while I'm not running autoionize. Then the requirement or memory goes
> up to 3.6 GB and after a while it crashes.

Yeah, I think that you're going to want to use a different ion placement
tool on this actually, as the autoionize plugin is going to need more memory,
and it'll take a long time to run on the 8 million atoms with all of
that water. Some of my colleagues and I have written another ion placement
tool that is probably better suited to your problem than autoionize is,
but still need to to package it up and post it. I'll ask Peter to post
about it. The main advantages are that it's all C/C++, runs in parallel
on shared memory machines using pthreads, and should work much better for
huge structures like you're working with.

> Maybe we can try the version of VMD that you're going to release,
> although I can wait for a couple of days if it coutd get you into some
> troubles. Hopefully this time it'll work out.

Yeah, after 1.8.5 is released I'll see what I can do to make you a
"lightweight" build of VMD that needs a less memory per atom.

  John 

-- 
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