Re: Fep questions about FepEquilSteps

From: Chris Chipot (Christophe.Chipot_at_edam.uhp-nancy.fr)
Date: Wed Apr 25 2007 - 16:25:11 CDT

Alex,

there are no "good" values or "bad" values. The amount of
equilibration you want to use is essentially dictated by
the transformation you are interested in. What you really
want to avoid is a lag between the Hamiltonian and the
configurations of your system, because the latter does
not immediately equilibrate in response to the perturbation
or change in the Hamiltonian. A good suggestion is to monitor
your ensemble average as a function of time and decide when
it is time to start accumulating the data that will contribute
to your free energy estimate.

Chris Chipot

alex digenova bravo a écrit :
> Hi all
> I have a questions about FEP, I am performing a Fep of Alanine to
> Aspartic Acids, I made three systems vacuo, solvate and lipid
> (membrane). I had very good result, but when I changed the value of
> FepEquilSteps variable (5000-good 10000-bad 20000-regular) my result
> changed. So my questions is What is a good value for FepEquilSteps
> variable?
>
> thanks!!!

_______________________________________________________________________

Chris Chipot, Ph.D.
Equipe de dynamique des assemblages membranaires
Unité mixte de recherche CNRS/UHP No 7565
Université Henri Poincaré - Nancy 1 Phone: (33) 3-83-68-40-97
B.P. 239 Fax: (33) 3-83-68-43-87
54506 Vandœuvre-lès-Nancy Cedex, France

                             E-mail: Christophe.Chipot_at_edam.uhp-nancy.fr
                                            http://www.edam.uhp-nancy.fr

        Greatness inspires envy, envy engenders spite, spite spawns lies
                                                 Joanne Kathleen Rowling
_______________________________________________________________________

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