AMBER Archive (2006)

Subject: Re: AMBER: klambda

From: David A. Case (case_at_scripps.edu)
Date: Mon Aug 14 2006 - 11:48:30 CDT

On Mon, Aug 14, 2006, Vitor Manuel Sousa F?x wrote:
>
> I am calculating the binding free energies between an
> artificial receptor and several cations and anions in an
> organic solvent using the thermodynamic integration
> methodology. The mutations involve only the change of vdw
> parameters, for example Na+ to K+ alone and in the
> presence of the receptor. In my case I obtain better
> results when a klamba=6 is used instead of klamba=1 (the
> agreement between the theoretical an experimental delta G
> solvation energies for the mutations M to M ´ in organic
> solvents are better for klamba=6. In the literature these
> type of transformations were usually reported with
> klamba=1. The question is the following: Is it
> scientifically acceptable undertake this type of
> transformation with klamba=1 ?...

This sounds like your free energies are not yet converged: you should get
the same overall energy for klambda=1 or 6. When making a small change like
that described above, I would expect klambda=1 to converge the most quickly.

There are, of course, lots of reasons why calculated values might not agree
with experiment. You first want to be sure that you have internally
consistent and converged calculated values.

...good luck...dac

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