From: L. Michel Espinoza-Fonseca (mef_at_ddt.biochem.umn.edu)
Date: Wed Aug 02 2006 - 17:04:07 CDT

Yeah, is what I thought about the Onyx, even though she's been a good girl :).

It'll be great to have such plugin to load this protein much faster! I
loaded a single snapshot of the molecule into VMD and I've been
waiting for almost 1.5 hrs! It gives me time to take a break and drink
some good coffee, but after some time it really annoys me...

BTW, I'm running the latest beta version of VMD 1.8.5 under Fedora 5.

Thanks!
Michel

2006/8/2, John Stone <johns_at_ks.uiuc.edu>:
>
> 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
>