Re: minimize in FEP....

From: Michael Grabe (
Date: Wed Apr 05 2006 - 12:56:36 CDT

Hi Raul

I would not minimize in each window - I would equilibrate but not
minimize. Hopefully your windows are physically close enough that
things are not too different in going from one to the other.

in general, the large dE values will be suppressed in the averaging. if
see lots of large dE values i would worry about something wrong in the
topology file or too large a time step or window size or something
like that.

i am not familiar with the oversampling method


On Apr 5, 2006, at 8:55 AM, Raul Araya wrote:

> De: [] En
> nombre de Raul Araya Secchi
> Enviado el: Martes, 04 de Abril de 2006 14:54
> Para:
> Asunto: namd-l: minimize in FEP....
> Dear NAMD users
> Im performing some FEP calculations but I have some problems and
> doubts.
> - If I put minimize in each window... does the minimizations goes
> according to lambda? or is just a minimization of the hibrid (dual
> topology) without considering the lambda valuie???
> - have any one used the Overlap Sampling method of FEP with NAMD?
> -what happens or what to do when some dE valuies are extremely High?
> just erase them? or considder that the run failed?
> Thanks
> Raul Araya
> CGB-Universidad Catolica de Chile
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Michael Grabe, Ph.D.
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