AMBER Archive (2009)

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

From: Hannes Wallnoefer (
Date: Wed Apr 08 2009 - 06:48:31 CDT

Hi Thomas,

I tried the suggestions you made and found that it depends on the number of
CPU´s i use.
When i do the simulation without the TI flags no problem occurs.
Also the TI transformation of the ligand works well (200k steps).
If i reduce the number of CPU´s to 2, all of the 200k steps are performed. With
8 CPU´s it stops after step 121900. The 4 CPU try is still running.

Do you think this is a mpd problem (as Ilyas mentioned)? What else could be the

Kind regards,

Zitat von

> 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
> big?
> 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
> here.
> Let me know if you find something,
> Kind Regards,
> Thomas
> Dr. Thomas Steinbrecher
> BioMaps Institute
> Rutgers University
> 610 Taylor Rd.
> Piscataway, NJ 08854
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> AMBER mailing list

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