About the correction of charging two ion water box by using FEP

From: Win Liu (mdsimulate_at_gmail.com)
Date: Mon May 28 2012 - 11:59:33 CDT

*Hi JC,*
*Thanks for the reply.*
2012/5/28 JC Gumbart <gumbart_at_ks.uiuc.edu>

> Read the paper of Hunenberger and McCammon carefully: they say that the
> inter-ion pmf is not affected dramatically by artifacts, which happen to
> cancel. ****
> **
    *I see your point.*

> My intuition is that you will have self-energy corrections for ion1 with
> ion1, ion2 with ion2, *and ion1 with ion2.*

> *Also the ion interaction between ion1 and ion2? Do you mean the
> interaction between ion1 and the ion2s from other boxes? In addition, in my
> case, what the parameter alchDecouple should be, on or off? If I set the
> alchDecouple on, the FEP will not include the Coulomb interaction between
> ion1 and ion2 in one box, but will include the self energy. Is my
> understanding correct? *

*Thanks a lot.*

> *From:* owner-namd-l_at_ks.uiuc.edu [mailto:owner-namd-l_at_ks.uiuc.edu] *On
> Behalf Of *Win Liu
> *Sent:* Monday, May 28, 2012 2:06 AM
> *To:* namd-l_at_ks.uiuc.edu
> *Subject:* namd-l: About the correction of charging two ion water box by
> using FEP****
> ** **
> Hi NAMD people,****
> ****
> I tried to charge two sodium atoms into two ions in water box by using FEP
> module. For one ion system, as written in FEP tutorial, there is a formula
> to estimate the artifatcs caused by the finite box size(PME artifacts)
> which was derived and explained in Gerhard Hummer's paper. So how about the
> artifacts in such two ions system? Actually, I read a paper written by
> Philippe H. Hünenberger and J. Andrew McCammon, J. Chem. Phys. 110, 1856
> (1999), in it, they concluded that in two identical ions system, artifacts
> caused by PME and PBC will be surprisingly almost 0. So is this means that
> the box size will not affect the value of free energy change in such
> process? But I tried the 30A and 70A size, the values are quite different--e89a8f22c41168ef7b04c11ba49a--

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