From: Chris Chipot (Christophe.Chipot_at_edam.uhp-nancy.fr)
Date: Thu Jun 08 2006 - 14:47:27 CDT
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
> 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!
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
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