AMBER Archive (2004)

Subject: Re: AMBER: General Question about AMBER's Free Energy Perturbation Method

From: Ilyas Yildirim (yildirim_at_pas.rochester.edu)
Date: Fri Dec 17 2004 - 15:53:07 CST

On Wed, 15 Dec 2004, David A. Case wrote:

> The people who are developing free energy methods in Amber (mostly me) generally prefer
> to use thermodynamic integration rather than free energy perturbation calculations, and
> this is what is supported in sander in Amber 7 and 8. Gibbs can still be used, but not
> with PME or with the generalized Born model, nor with potentials that use "extra points".
> For these reasons, I believe that gibbs is no longer the program of choice for carrying
> out the sorts of simulations you describe.
>
> ...good luck...dac
>

Dear Prof. Case,

Is there any sander tutorial which uses the TI Method? (Or any paper which
uses the TI Integration method to calculate the Free Energy Difference of
two structures)

Thanks.

Ilyas Yildirim

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