From: Ana Celia Vila Verde (acavilaverde_at_gmail.com)
Date: Thu Aug 29 2013 - 04:07:02 CDT
Hi everyone,
I'm using NAMD to run simulations where polarizability is explicitly
included through the Drude model. According to
http://www.ks.uiuc.edu/Research/Drude/,
" The screened Coulomb correction of Thole is calculated between
atom-Drude pairs that are otherwise excluded from nonbonded interactions."
To verify that intramolecular electrostatic interactions were indeed
always calculated between 1-3 Drude pairs when "exclude1-3" was selected
, I ran two test cases using a simple model of the sulfate ion (see
pubs.acs.org/doi/abs/10.1021/jp4059802) and I found some puzzling
results. The oxygens in the model are polarizable, i.e. they consist of
a pair of Drude charges, but the sulfur is not.
Case 1 (attached file 001_dip0.zip): a single sulfate ion in its
equilibrium configuration (i.e., when S is at (0,0,0), the net dipole
moment of the ion is 0)
In this case, the electrostatic energy of the system is zero, indicating
that intramolecular electrostatic interactions are NOT calculated,
contrary to what is stated in http://www.ks.uiuc.edu/Research/Drude/
Case 2 (attached file 003_dipNON0.zip): a single sulfate ion identical
in most aspects to that used in Case 1. The only difference now is that
the drude particles are not in their equilibrium position, so the net
dipole moment of the sulfate is not zero.
In this case, the electrostatic energy of the system is NOT zero.
However, it is also not what it should be if NAMD were calculating the
interactions between intramolecular drude pairs using Thole screening
functions. So, NAMD is calculating some sort of intramolecular energy
in this case, but what?
Can anyone explain exactly how NAMD calculates intramolecular
electrostatic interactions between Drude pairs? The files I used to
run the two test cases are attached in case anyone wants to look into
this more closely.
Best,
Ana
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