VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Tue Aug 22 2006 - 19:02:12 CDT

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