On 10/12/16 5:32 PM, Nash, Anthony wrote:
I¹m trying to fine tune the rdf of tip3p water molecules around a central
metal dummy molecule ("Force Field Independent Metal Parameters Using a
Nonbonded Dummy Model²), essentially a central metal (with vdw parameter
and -1 charge) covalently bonded to six Œdummy¹ atoms (no vdw parameters,
each with a +0.5 charge). Despite all my efforts at recreating the RDF
from the published work, my first peak deviates by almost 0.8 Angstroms.
The original publication showed that a deviation from their rdf resulted
in a large deviation from the correct solvation free energy. Also, a metal
demonstrating a deviation of around 0.8 angstrom in a water box will more
than likely prevent the metal from settling in plane to the nitrogen atoms
of a heme group when the parameters are put into practice.
I have looked into adjusting the following in my attempt at bringing the
first hydration shell closer to the dummy atom:
-adjusting the sigma & epsilon (started from the published values I¹ve
iteratively gone through tens of paired values, with sigma never getting
below 0.48129. Any attempt at doing so causes steepest descent to crash
during an energy minimisation)
-shortened the equilibrium bond lengths of the central metal atom to its
bonded dummy atoms
-increased the positive charge on the dummy atoms whilst reducing the
negative charge on the central metal atom
0.32 Angstrom is as close as I can get it without the energy minimisation
from crashing out (excessive force).
A bit of a long shot but any suggestions on how I could tune these
What do the authors say when you tell them you can't reproduce their published
Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow
Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201
jalem...@outerbanks.umaryland.edu | (410) 706-7441
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