From: jz7_at_duke.edu
Date: Thu Jun 08 2006 - 15:28:21 CDT
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
>
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>
> N. G. van Kampen
> _______________________________________________________________________
>
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