From: Jason Swails (jason.swails_at_gmail.com)
Date: Wed Apr 03 2013 - 15:58:21 CDT
Hello everyone,
I have a question about how pairwise electrostatic interaction energies are
calculated when using PME. What I want to do is to calculate the energy of
a single water molecule with every other atom in the system (as a way of
approximating a one-step FEP free energy in which I annihilate the water).
I can set up the calculation just fine and I even get back reasonable
numbers.
What I can't figure out, though, is where the number comes from. I
understand that the reciprocal space sum is not pairwise decomposable (and
Axel says as much here:
http://www.ks.uiuc.edu/Research/namd/mailing_list/namd-l.2009-2010/4161.html).
Nevertheless, NAMD gives me reasonable numbers. I can envision this
calculation being done in one of two ways (admittedly not much thought has
been put into alternatives):
1) Forget about the reciprocal space sum, just decompose the direct space
sum. Use a large direct-space cutoff and a diffuse neutralizing charge
distribution and call it good enough.
2) Perform 2 Ewald calculations: one with the whole system and the other
with the single water molecule given charges of zero, then take that
difference... or something along those lines. (Maybe you need a 3rd, where
the surroundings are given a charge of 0 and the water has a charge?)
I'm guessing the approach actually taken is (1), but I haven't been able to
find any documentation or discussions on the mailing list actually stating
this.
Any help is appreciated.
Thanks!
Jason
-- Jason M. Swails Quantum Theory Project, University of Florida Ph.D. Candidate 352-392-4032
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