On 7/25/14, 12:40 PM, Tamas Karpati wrote:
Dear Justin,
Thanks for your educational answers.
Coulombic interactions fail at short distances; you probably need to apply
I was afraid of that... somehow removing shells from the cores in the
initial structure have let it "functionally" work (with not yet
reasonable results).
Thole screening to avoid polarization catastrophe. Ions are particularly
problematic in this regard.
I've seen this mentioned in the Manual, but hadn't ever hit GROMACS
specific details on how to apply polarization in the input files.
The only source I could locate is within the GROMACS package,
under the name "sw.itp". It does exclusively implement the
so called "water polarization" model -at least I think so.
The "water polarization" function is a water-specific anisotropy function.
Don't try to use it for anything else; the interpretation of the atom numbers
for local axis construction are very specific.
Can you please direct me to a source from which I could learn
how to polarize GROMACS? I was'not lucky on the Internet and,
indeed, even at the GROMACS site or Manual (neighter application
examples nor file format descriptions).
The Thole screening function is (in the released version) not used by anything,
so it's not documented. In its present incarnation, you need a
[thole_polarization] directive that lists atom-shell/Drude pairs as follows:
atom_i shell_i atom_j shell_j 2 a alpha_i alpha_j
The "2" is a required function type. My implementation of the CHARMM Drude FF
is nearly done, and there are changes to the way the Thole directive is laid out
in the future, but at the moment (up through version 5.0), this is the way it
works. The code is in src/gromacs/gmxlib/bondfree.c.
-Justin
--
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Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow
Department of Pharmaceutical Sciences
School of Pharmacy
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http://mackerell.umaryland.edu/~jalemkul
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