Re: question about total charge change in FEP calculation

From: Jerome Henin (jhenin_at_vitae.cmm.upenn.edu)
Date: Fri Jun 09 2006 - 10:20:01 CDT

The free energy for such an alchemical transformation is likely to be very
large, however, that quantity has no direct physical relevance. You will get
a meaningful value by running another alchemical transformation (e.g. in
vacuum) and substracting the two deltaG.

Jerome

On Thursday 08 June 2006 16:28, jz7_at_duke.edu wrote:
> This time I just turn the chloride ions to nothing, and add positional
> restraints (as before) to the FEP simulation. However, I still got large
> free energy change (the same scale as before). How to fix/improve the
> results? Really appreciate the help.
>
> Sincerely,
> Jeny
>
> On Thu, 8 Jun 2006, Chris Chipot wrote:
> > Jeny,
> >
> > I would simply turn the chloride ions to nothing, rather than
> > perturbing them into water. To prevent the ions from getting
> > exceedingly close to the solute, I would add some positional
> > restraints.
> >
> > Chris Chipot
> >
> > jz7_at_duke.edu wrote:
> > > Dear Dr. Chipot,
> > >
> > > Now my FEP simulation in NAMD works. For a test case (change of lambda
> > > is 0.1 for each window), the accumulated net free energy change is huge
> > > (about 300 from the fepout file). I guess if I decrease the delt_lambda
> > > to 0.01 for each window and increase the equilibration and sampling
> > > steps, I could get a more reasonable result, right?
> > >
> > > However, I have some concern about the counter-ions. Since my system
> > > involes total charge change during the FEP simulation, I also change
> > > two Cl ions to water molecules to compensate the total charge change,
> > > such that the system is always neutral. I did add some contraints to
> > > those two Cl and the oxygen atoms to constraint them at the same
> > > position. But how much energy contribution from the ion-to-water
> > > mutation from the simulation should I expect? I guess I should exclude
> > > the solvent contribution to get the result comparable with experiment?
> > >
> > > Thanks a lot!
> > >
> > > Jeny
> >
> > _______________________________________________________________________
> >
> > Chris Chipot, Ph.D.
> > Equipe de dynamique des assemblages membranaires
> > Unité mixte de recherche CNRS/UHP No 7565
> > Université Henri Poincaré - Nancy 1 Phone: (33) 3-83-68-40-97
> > B.P. 239 Fax: (33) 3-83-68-43-87
> > 54506 Vand?uvre-lès-Nancy Cedex
> >
> > E-mail: Christophe.Chipot_at_edam.uhp-nancy.fr
> > http://www.edam.uhp-nancy.fr
> >
> > Science without management is worse than management without science
> >
> > N. G. van Kampen
> > _______________________________________________________________________

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