AMBER Archive (2009)

Subject: [AMBER] TI production runs stop after a certain Step number

From: Hannes Wallnoefer (
Date: Tue Apr 07 2009 - 06:48:45 CDT

Hi all,

I am doing TI calculations in Amber10 with the soft core potential method. I
followed the tutorial and just changed the forcefield (99SB instead of ff03).
The minimization and the equilibration was ok in any case, but the production
run for the complexes stopped after step 81900. This happens reproduciblly with
any lambda value and in any of the three steps (charge removal, vdW
transformation, and recharging). If i restart the produvtion run after step
80000 it makes another 81900 steps and again stops. Stop doesn´t mean that it
stalls, but it simply doesn´t write any output any more, although all of the
CPU´s (i use sander.MPI with 16 cores) have a load of 100%.
If i reduce the number of steps to 80000 for any proudction run i get a similar
result as described in the tutorial and everything seems to run without any
I also tried another example than the T4 lysozyme from the tutorial and observe
the same behaviour.
Does anybody have an idea what happens? Is there something like an internal step
number limit (81900 seems a little bit strange)? Could there be a problem with
the compilation? Is there another important information i should provide?

Best regards,

AMBER mailing list