From: Chris Chipot (Christophe.Chipot_at_edam.uhp-nancy.fr)
Date: Wed Jun 08 2005 - 17:59:42 CDT
Dear Shahid,
to run a reverse FEP calculation signifies that ? goes from 1 to 0,
if it went from 0 to 1 in the forward run. In other words, you ought
to use the last configuration, at the end of your direct "alchemical
transformation", as the starting point of your reverse simulation.
You can of course do that in terms of a direct simulation, modifying
the FEPfile. Atoms that were declared to vanish (-1) will now appear
(+1), and vice versa. The difference (hysteresis) between the free
energy curves ?Ga?b and ?Gb?a as a function of ? is expected to
provide you with an estimate of the error associated to your
calculation. Keep in mind, however, that differences in the
convergence properties of free energy calculations may result
in the fact that the reverse transformation does not necessarily
converge to -?Ga?b. Such is the case, for instance, of the
well-known particle insertion problem of Widom. Whereas the direct
simulation converges towards the excess chemical potential, the same
cannot be said for the reverse transformation.
Chris Chipot
Shahid Qamar wrote:
> Hi,
> I am running a free Energy Perturbation on a system. I am reading in
> the literature that I have to do reverse FEP. What does that mean and
> how I can run reverse FEP? Is it just to change the ID in the B column
> from 1 to -1 and make the initial state at the final state and vice
> versa and then run the FEP or something else?
> If someone have ay idea then please let me know.
> Thanks for your help.
>
> Regards,
>
> Shahid Qamar
_______________________________________________________________________
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 Vandoeuvre-lès-Nancy Cedex
E-mail: Christophe.Chipot_at_edam.uhp-nancy.fr
http://www.edam.uhp-nancy.fr
To sin by silence when we should protest makes cowards out of men
Ella Wheeler Wilcox
_______________________________________________________________________
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