NAMD: Exiting Prematurely

From: Arun Krishnan (
Date: Tue Aug 14 2007 - 19:59:54 CDT

Dear All,

I seem to be running across this weird error. I am trying to unfold a small
protein. I use the following protocol:

a) energy minimization of protein + water box
b) heat to 300K
c) equilibration for 50ps
d) Production run for 1ns

e) Heat to 500K
f) equilibrate
g) production run

All the steps from a-f seem to go fine. I followed the
temperature/pressure/energy profiles for each step
and they seem to be fine. However for step (g), the program ends abruptly
with an "Exiting Prematurely"
message. That's it.. no other error messages. This happens about 2ps into
the simulation. I am using an NVT
ensemble.. I checked the temperature/volume/pressure/energy and all are
stable. There are no sudden drops
of any sort.. The only sudden change I found was during stage (f) where the
total energy during the equilibrate stage
at 500K rose from -71000 to -66500 or thereabouts and then remained stable.

I also checked the DCD file for the production run at 500K and I don't see
anything out of the ordinary. The protein
is still well within the waterbox. Am at a loss to understand what could be
causing the sudden crash. Is there a way
to find out more about what caused the premature exit?



Arun Krishnan, Ph.D,
Assistant Professor,
Institute for Advanced Biosciences,
Keio University,
Center Building,
Tsuruoka, Yamagata 997-0035
Phone: +81 (0)235-29-0824

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