VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_cmm.chem.upenn.edu)
Date: Tue Aug 22 2006 - 18:10:54 CDT

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.