AMBER Archive (2004)

Subject: Re: AMBER: free energy perturbation

From: David A. Case (case_at_scripps.edu)
Date: Tue Apr 06 2004 - 20:26:37 CDT

On Tue, Apr 06, 2004, Herbert Georg wrote:
>
> I would like to perform a free energy perturbation calculation in which
> the free energy difference refers to inclusion of a molecule into
> another. It doesn't change its atom type, element or charge but only
> moves from the inside to the outside of the host molecule. Is this
> possible to do with AMBER??

As others have mentioned, this sort of calculation is better supported in
Amber 8 (no special programming generally required) than in earlier versions.

Even if you don't (yet!) have Amber 8, you can get an idea of what is
involved [and potentially enough info to do this yourself in earlier versions
of the code] by looking at section 5.15 of the Amber 8 Users' Manual, which
is available from the Amber web site.

...good luck...dac
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