VMD-L Mailing List

From: L. Michel Espinoza-Fonseca (mef_at_ddt.biochem.umn.edu)
Date: Tue Aug 22 2006 - 17:36:39 CDT

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