AMBER Archive (2009)

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

Date: Tue Apr 07 2009 - 09:49:57 CDT

Hi Hannes,

> I am doing TI calculations in Amber10 with the soft core potential method.
> 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
> Does anybody have an idea what happens? Is there something like an
> internal step number limit (81900 seems a little bit strange)? Could

This sounds very odd indeed. Seeing the same behaviour in charge removal
and vdw steps means its not connected to the softcore module because you
would not be using that in the former case. There is no internal limit in
the number of steps in any of the amber function that I am aware of (and
it is certainly not 81900...). Since you can run 2x80.000 steps
consecutively and pass over the 81900 error mark without trouble (I read
that you can do that from your description) my best guess would be that
this is less an amber but an OS problem. Maybe Your queueing system hits a
cutoff at that point? Or some filesize limit is passed if your system is

Can you ran your system for 100k steps without using TI? Can you run a
very small TI system (say the toluene to nothing example from the tests)
for 100.000 steps? Does the same problem occur on only two processors?
Sounds like a hard to track down problem, I'm more or less just guessing

Let me know if you find something,

Kind Regards,


Dr. Thomas Steinbrecher
BioMaps Institute
Rutgers University
610 Taylor Rd.
Piscataway, NJ 08854

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