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

From: JC Gumbart (
Date: Mon May 28 2012 - 08:41:56 CDT

Read the paper of Hunenberger and McCammon carefully: they say that the
inter-ion pmf is not affected dramatically by artifacts, which happen to


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



From: [] On Behalf
Of Win Liu
Sent: Monday, May 28, 2012 2:06 AM
Subject: namd-l: About the correction of charging two ion water box by using


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.


The best wishes.


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