Re: FEP....

From: Chris Chipot (
Date: Fri Nov 11 2005 - 10:35:19 CST

You can certainly run an energy minimization prior to staring
the FEP calculation per se. I fail to see the point of running
a minimization step at each ?-state. Either your system is in
a local minimum of the potential energy surface or it is not,
in which case you should remedy this. It is important, however,
that ample equilibration be run to prevent your Hamiltonian
from lagging behind.

Chris Chipot

> Hello NAMD Users....
> Im wondering if anybody knows if one can set up an alchemical FEP
> calculation with a minimization step prior to the equilibration and
> production stage?
> Please help....
> Raul


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 VandSuvre-lès-Nancy Cedex


      To sin by silence when we should protest makes cowards out of men
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