VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Wed Aug 02 2006 - 16:53:53 CDT

Michel,
  The opteron will be a much faster machine for visualization and
analysis since the old Onyx machine has (by today's standards)
very slow processors in it. What file format was your structure
stored in? If you're working with NAMD, you'll get the best results
by loading your PSF file first, and then loading the PDB/DCD second.
Doing things in some other order will be slower and eat more memory.

While you have VMD open on the Opteron with the big file loaded,
see how much memory it is using using the 'top' command (assuming
that you're running Unix on this machine). If you can do that and
report back the numbers, I can give you some suggestions for getting
further performance increases.

If it is mainly the file loading time for PSF/PDB that is slow,
I could give you a special binary molecule file plugin
so you can load this thing MUCH faster during your day-to-day work.
I forgot to ask, which version of VMD are you using currently?

  John Stone
  vmd_at_ks.uiuc.edu

On Wed, Aug 02, 2006 at 04:41:16PM -0500, L. Michel Espinoza-Fonseca wrote:
> Hi John,
>
> Thank you for your reply. I'm actually going to simulate such a big
> system with NAMD and further analyze it with VMD. I'm really concerned
> about this, because I tried to load a single structure on my
> workstation (Opteron, 2Gb RAM) and it took really long time. I have
> access to more robust visualization facilities (a SGI Onyx4, 16
> processors, 32 Gb RAM), so maybe I could use it for visualization and
> analysis. What do you think?
>
> Concerning the connectivity info, I'll be using a psf file +
> trajectory in dcd format. Considering what you told me, I think that
> I'll save a lot of time :)
>
> Thank you for your help!
> Michel
>
> 2006/8/2, John Stone <johns_at_ks.uiuc.edu>:
> >
> >Michel,
> > VMD can load structures that large with no problem if you have enough
> >memory, say 2 to 3GB. The main remaining issue after memory is that
> >you'll be able to load such a structure MUCH faster if you use a file
> >format that contains bond/connectivity information. If there's no
> >connectivity info (e.g. lone PDB), then VMD will have to do a bond
> >search after the file is loaded, and that can take a long time on
> >really really large structures.
> >
> >With a structure that large, I highly recommend using the
> >Points, NewRibbon, and NewCartoon representations since they'll work better
> >for things of that size. If I knew more about your structure and what
> >you want to do with it once in VMD, I could give you more suggestions on
> >getting it loaded and displayed most efficiently. Let me know if you
> >need more help.
> >
> > John Stone
> > vmd_at_ks.uiuc.edu
> >
> >
> >On Wed, Aug 02, 2006 at 03:25:41PM -0500, L. Michel Espinoza-Fonseca wrote:
> >> Hi John,
> >>
> >> I was wondering about what's the maximum number of atoms that VMD can
> >> handle. Currently, I have a system of about 6.5 million atoms, so I
> >> would like to know if I'll be able to visualize it :)
> >>
> >> Thanks!
> >> Michel
> >
> >--
> >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