AMBER Archive (2006)

Subject: Re: AMBER: klambda

From: Ilyas Yildirim (yildirim_at_pas.rochester.edu)
Date: Mon Aug 14 2006 - 12:31:24 CDT

If your transformation is smooth enough to integrate (dv/dl vs. l), I
think your result is ok. How many lambda values did u use, and how does
the dv/dl vs. l graph (where l stands for lambda) look like?

On Mon, 14 Aug 2006, Vitor Manuel Sousa F?x wrote:

> Dear Amber users
>
> 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 ?...
>
> Thanks a lot in advance for your help
>
> Vitor Felix
>
>
> *****************************
> Vitor Felix
> Department of Chemistry
> University of Aveiro
> 3810-193 Aveiro
> Portugal
> Tel: 351 234 370 729
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> 

-- 
  Ilyas Yildirim
  ---------------------------------------------------------------
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