VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Thu Aug 24 2006 - 21:52:35 CDT

Hi,
  I've posted a preliminary distribution of the parallel ion placement tool
into the VMD (Public) project on BioCoRE, in the 'ionize' subdirectory.
You can get access via this page if you don't have a biocore account already:
  http://www.ks.uiuc.edu/Research/vmd/alpha/

While the built-in autoionize plugin would eventually do the job, I think
for the 8 million atom structure you're going to want to use this new tool
(which will eventually be integrated into the VMD plugins as well..)
as it will run MUCH faster, particularly on recent Intel/AMD chips with
SSE3 vectorization support (you'll probably need compile with the
Intel C/C++ compilers to take advantage of that).

  John Stone
  vmd_at_ks.uiuc.edu

On Thu, Aug 24, 2006 at 01:17:30PM -0500, L. Michel Espinoza-Fonseca wrote:
> 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
> > 

-- 
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