From: John Stone (
Date: Wed Feb 08 2012 - 10:06:45 CST

  I just sent the following query to Michael Doig, if you let me know the
same information I may be able to provide some suggestions to workaround
the problem:

  What platform are you running VMD on? This seems to be an issue related
to deep recursion running out of stack space, which is a problem that tends
to crop up some platforms more than others, and sometimes you can get around
it simply by setting an environment variable. If you can tell me what
platforms you're using, I can provide you with some suggestions to try out.

  John Stone

On Wed, Feb 08, 2012 at 08:11:21AM -0500, Yamada, Masako (GE Global Research) wrote:
> I'm facing the same issue that Michael Doig posted recently. I've tried
> the most recent non-beta VMD 1.9.1 build (Feb 04, 2012) and continue to
> get a segmentation fault during write-out. Reading the core dump using a
> debugger, I get similar output to what Michael Doig posted.
> For your reference, I've attached the two Tcl (topotool) scripts that I've
> been using. Pls run "tip3p_hemisphere.tcl" first to generate the PDF file
> and then "pdbtolammps_noshift.tcl" to convert to LAMMPS format. This works
> fine, until the number of atoms becomes on the order of 10^6. To add to my
> confusion, I could've sworn these exact scripts previously WORKED using a
> million atoms. I have a million-atom LAMMPS file on hand to prove it.
> Masako Yamada, Ph.D
> GE Global Research

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