Re: simulation crashing with nan

From: Peter Freddolino (petefred_at_ks.uiuc.edu)
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.

Best,
Peter

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
>
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