AMBER Archive (2004)

Subject: Re: AMBER: free energy perturbation

From: David Smith (
Date: Tue Apr 06 2004 - 10:45:06 CDT

Hi Herbert,

What you are referring to is called a potential of mean force and is the
free energy change for a conformational rather than a compositional
change. Various versions of AMBER can handle this in various different
ways. It is not trivial but take a look at gibbs in versions 6 and 7. I
didn't upgrade to 8 yet so can't comment on what's there but I
understood that this functionality was going to be introduced into

Good luck.

Dr. David Smith
Rudjer Boskovic Institute
Bijenicka 54
10002 Zagreb, Croatia
tel: +385-1-4561117
fax: +385-1-4561118

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