VMD-L Mailing List

From: L. Michel Espinoza-Fonseca (mef_at_ddt.biochem.umn.edu)
Date: Wed Aug 02 2006 - 16:41:16 CDT

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
>