NAMD terminates prematurely without error.

From: Ajasja Ljubetič (
Date: Wed Jun 23 2010 - 02:41:24 CDT

Hello all,

While running NAMD on a specific protein system namd sometimes just stops.
There are no errors or warnings written in the log file and no indication
that something went wrong otherwise. But the trajectory is not complete.
When I restart sometimes the simulations stops after a few seconds and
sometimes it runs for a few hours and stops again. I have tried running it
on different nodes of our toy cluster, but with similar results. Other
programs and other protein systems in NAMD seem to run just fine.
What could causing such behaviour?

I am running a simulation of a protein with a fixed backbone in vacuo (I am
only interested in the space the side-chains use and I have run the same
protein in water to compare the results).
I am running namd 2.7b2 for win32 on winXP. I have tested the RAM (when
installing the computers about 3 months ago) as well as the hard drive and
stress tested the CPU.
I am attaching the configuration file used to run the simulation as well as
what I'm using to restart it and a log file of a run that just stopped.
Any hints are appreciated, as this restarting is quite bothersome (what
should be finished in 16 hours I am all ready running for two days).

thank you and best regards,

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