Re: simulation crashing with nan

From: Peter Freddolino (
Date: Wed Jul 26 2006 - 10:12:52 CDT

Hi Jackie,
this is usually a sign of a pathological starting structure, for
example, one with two atoms at the exact same coordinates, or a periodic
cell size that is too small. Could you be more specific about how you
set up your simulation?

Also, this is a minor point, but please try to avoid using .doc files
for passing information on the mailing list; these will not be easily
readable to everyone.


Jackie wrote:
> Hi all,
> I'm sorry about people having to repeat this. I saw some info about
> this in the namd mailing list, but I didn't quite understand what to
> do. This is the error I have when trying to run the simulation. It
> appears in the log file and is in the attachment.
> Thank you very much,
> Jackie
> ------------------------------------------------------------------------
> Talk is cheap. Use Yahoo! Messenger to make PC-to-Phone calls. Great
> rates starting at 1/min.
> <**>

This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 15:42:24 CST