Date: Thu Jun 08 2006 - 10:16:23 CDT
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!
On Fri, 26 May 2006, Chris Chipot wrote:
> > In you last email, you also mentioned that for such system (total charge
> > change during FEP), "one possible way is to fix or restrain the
> > counter-ions spatially to prevent them to come too close to the perturbed
> > titrable sites". I am not sure how to do this techniquely (the charge
> > distribution of the starting&ending states should be different). Could you
> > please explain more in detail?
> One possibility is to use "constraints" for harmonic restraints, or if
> you want to freeze the positions, "fixedatoms".
> You may want to post your future questions to the namd-list, as they
> might interest the rest of the community.
> 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
> Science without management is worse than management without science
> N. G. van Kampen
JIERU ZHENG Phone: (919) 660-1634
Department of Chemistry Fax: (919) 684-4212
Duke University Email: jz7_at_duke.edu
Durham, NC 27708
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