AMBER Archive (2004)

Subject: Re: AMBER: GIBBS: FEP and TI

From: David A. Case (
Date: Wed Mar 31 2004 - 13:07:17 CST

On Mon, Mar 29, 2004, Miguel de Federico wrote:
> I would like to do a rather basic question... Could any body suggest me some
> literature about Thermodynamic Integration method for evaluating free energy
> differences? Is there any comparison between Window Growth and Thermodinami
> Integration?

There is lots of literature on this subject, and you should carefully read
the section called "Choices affecting free energy calculations" of the (Amber
7 and earlier) Users' Manual.

I think that in almost every case, thermodyanmic integration is the method
of choice for "alchemical" changes. This is in fact the only method supported
in current versions of Amber.

...hope this helps...dac


================================================================== David A. Case | e-mail: Dept. of Molecular Biology, TPC15 | fax: +1-858-784-8896 The Scripps Research Institute | phone: +1-858-784-9768 10550 N. Torrey Pines Rd. | home page: La Jolla CA 92037 USA | ================================================================== ----------------------------------------------------------------------- The AMBER Mail Reflector To post, send mail to To unsubscribe, send "unsubscribe amber" to