From: JC Gumbart (gumbart_at_ks.uiuc.edu)
Date: Mon May 28 2012 - 17:15:35 CDT
Thinking about it again, it probably doesn't matter. The self-energy is a sum over individual charges, so I think the correction for two separate charges should be 2*(1/2*\xi_EW (1^2-0^2) = \xi_EW. Of course, you can check this yourself.
I would use alchDecouple on, in which case I think the two ions will interact with each other, but these interactions will not change during the simulation so they won't contribute to the free energy. But really, this seems to be a bit of an odd simulation, so I recommend thinking very carefully about what you should expect to happen.
On May 28, 2012, at 11:59 AM, Win Liu wrote:
> 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.
>
>
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> 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.
> Wenhao
>
> 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. So can anyone point out my fault? Thanks a lot.
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> The best wishes.
>
> Wenhao
>
>
>
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