VMD-L Mailing List

From: L. Michel Espinoza-Fonseca (mef_at_ddt.biochem.umn.edu)
Date: Thu Aug 24 2006 - 13:17:30 CDT

Hi Guys,

Thank you for your help. I'll try that new ionization tool you
mentioned, even though it would be nice to see how well autoionize
works with huge systems.

BTW, I'm happy you liked the system, John! I also liked it the first
time I solvated it, it feels like that's your little kid :)

Cheers,
Michel

2006/8/22, John Stone <johns_at_ks.uiuc.edu>:
>
> 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
>