VMD-L Mailing List

From: L. Michel Espinoza-Fonseca (mef_at_ddt.biochem.umn.edu)
Date: Mon Aug 21 2006 - 20:49:27 CDT

Hi John,

I've been trying to solvate a system using the plugin solvate. This
system is really big, so when it is almost going to finish, I get the
following message:

Info: segment complete.
Info: writing psf file sys1-water.psf
total of 7526004 atoms
total of 5434576 bonds
total of 4309388 angles
total of 3228210 dihedrals
total of 209070 impropers
total of 77670 cross-terms
Info: psf file complete.
Info: writing pdb file sys1-water.pdb
Info: pdb file complete.
psfplugin) Detected a Charmm31 PSF file
Info) Using plugin psf for structure file microtubule-water.psf
terminate called after throwing an instance of 'std::bad_alloc'
  what(): St9bad_alloc
Abort

And that's all. Do you have any hint on what would be the problem? I'm
using a workstation with 2 double-core Opteron processors,4 GB RAM.

Thanks!

Michel