Re: [AMBER] TI in vacuum

From: <>
Date: Tue, 8 Feb 2011 04:57:30 -0500 (EST)


> - where it was lambda=0.4, I change to 0.42, and where it was lambda=0.1,
> I
> change to 0.12. In both cases the simulations went well until the end.

to me this indicates that something happens in your structure which causes
the problem. Changing lambda gives you a slightly different trajectory and
the problem might then occur at a different point in the trajectory or not
at all.

> the
> simulation ran with lambda=0.099....

When you make such tiny changes the potential energy landscape almost
doesn't change, but again the trajectory will be different after a few
hundred steps. Is it possible to write out the trajectory after each
mdstep for both processes at l=0.1 and 0.0999? Then you could compare what
happens in the first simulation right before it fails compared to the
second one which works ok.

Kind Regards,


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

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Received on Tue Feb 08 2011 - 02:00:03 PST
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