VMD-L Mailing List

From: L. Michel Espinoza-Fonseca (mef_at_ddt.biochem.umn.edu)
Date: Tue Aug 22 2006 - 19:16:29 CDT

John, Axel,

Thanks for the comments! I'll test it now using the -debug option and
see what comes out. I also think it can be because I'm running out of
memory (sad, indeed very sad!).

I'll let you guys know what I got. Anyway, I'll upload the structure to biocore.

Enjoy!
Michel

2006/8/22, John Stone <johns_at_ks.uiuc.edu>:
>
> Hi,
> Yes, Axel has a good suggestion, in that running VMD with
> 'vmd -debug' will allow you to track down the location where the crash
> occurs, though if it's running out of memory (likely), the real cause
> may be a bad piece of code that goes superlinear, or even O(N^2) with
> the number of atoms. I've personally run into this with certain plugins,
> or script with very large structures before, so it's possible you found
> another case that we didn't already know about. In any case, I'll look
> at your structure(s) as soon as they are posted and I'm back at the lab.
>
> John
>
> On Tue, Aug 22, 2006 at 07:10:54PM -0400, Axel Kohlmeyer wrote:
> > michel,
> >
> > nobody here has psychic capabilities or the ability to remember
> > all of your posts over the last months, so please answer the
> > (usual) questions:
> > - what version of VMD are you using?
> > - what platform are you running on?
> >
> > please try to run vmd with the -debug option, so
> > that we can see _where_ the problem is happening.
> >
> > regardless, i would recommend to check the generated
> > files _very_ carefully, because i don't expect that all plugins
> > in VMD have been tested on such large systems.
> >
> > thanks,
> > axel.
> >
> > On 8/22/06, L. Michel Espinoza-Fonseca <mef_at_ddt.biochem.umn.edu> wrote:
> > >Hi John,
> > >
> > >It's me again. This time I got a problem where I'm unable to get any
> > >solution. I'm trying to add ions to a fairly big system (this time
> > >something around 8,000,000 atoms). I can solvate it with no problems,
> > >but when I try to run autoionize, I get the following:
> > >
> > >reading topology file
> > >/home/bscl2/espinoza/lib/vmd/plugins/noarch/tcl/autoionize1.2/ions.top
> > >>>>>>> SOD and CLA Ions Topology File <<<<<<<<<
> > >extracted from
> > >>>>>>>>>CHARMM22 All-Hydrogen Topology File for Proteins <<<<<<
> > >>>>>>>>>>>>>>>>>>>>>> August 1999 <<<<<<<<<<<<<<<<<<<<<<<<<<<<<
> > >>>>>>>> Direct comments to Alexander D. MacKerell Jr. <<<<<<<<<
> > >>>>>>> 410-706-7442 or email: alex,mmiris.ab.umd.edu <<<<<<<<<
> > >
> > >Created by CHARMM version 27 1
> > >
> > >Autoionize) Reading monster-water.psf/monster-water.pdb...
> > >clearing structure, preserving topology and aliases
> > >reading structure from psf file monster-water.psf
> > >reading coordinates from pdb file monster-water.pdb
> > >psfplugin) Detected a Charmm31 PSF file
> > >Info) Using plugin psf for structure file monster-water.psf
> > >Segmentation fault
> > >
> > >And of course VMD crashes. I made stacksize and coredumpsized
> > >unlimited, but I got the same thing (VMD crashes). Do you have any
> > >suggestions on how to solve the problem? I'm using a workstation with
> > >2 double-core Opteron and 4 GB of RAM.
> > >
> > >Thanks!
> > >
> > >Michel
> > >
> > >
> >
> >
> > --
> > =======================================================================
> > Axel Kohlmeyer akohlmey_at_cmm.chem.upenn.edu http://www.cmm.upenn.edu
> > Center for Molecular Modeling -- University of Pennsylvania
> > Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323
> > tel: 1-215-898-1582, fax: 1-215-573-6233, office-tel: 1-215-898-5425
> > =======================================================================
> > If you make something idiot-proof, the universe creates a better idiot.
>
> --
> 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
>