On 7/29/14, 9:33 AM, Tamas Karpati wrote:
Dear Justin,
I've tried applying the [thole_polarization] section in
the format you've suggested. I've noticed the followings.
1. First I made a mistake and forgot to remove the [polarization]
section from the TOP file. Even this way MDRUN worked and indicated
the usual ca. 10 kJ/mol contribution from polarization.
Besides a new contribution of ca. 600 kJ/mol appeared from Thole pol.
I switched the former off to have just one kind of pol effect.
Is this correct?
No, they're not mutually exclusive. The Thole function screens nearby dipoles
so they don't experience artificial forces. The "thole_polarization" name is a
bit unfortunate; it should really be "thole_screening" instead.
I suspect you're seeing large forces due to one (or more effects). If your
model doesn't have any bonds, then you don't have any excluded interactions, so
instead of getting a screened Coulombic interaction via Thole screening, you're
getting both added together. You should make use of [exclusions] for
neighboring pairs, likely, but I guess the bigger question is how your force
field was parametrized and what its expected behavior should be.
The other effect is one that I noticed this weekend. I think the forces coming
out of the Thole function are incorrect; at least they are in the case of our
Drude polarizable force field. I changed the force calculation and everything
works as expected now, in my development version of the code.
2. I assumed that in the [thole_polarization] section of the TOP
file I needed to select which dipole pairs are to be included on
basis of my "chemical intuition" -if I had any. I tried a few radii
of "sphere-of-inclusion" but saw little differences.
Is it a correct selection for Thole screening? (I have a crystal
with separate ions held together by Buckingham forces and Thole
polarization -there are no bonds at all.)
Do I have a way to switch on/off intercell dipole interactions?
I don't know what the right answer is here. What is the source of the force
field parameters? In our Drude model, 1-2 and 1-3 interactions (based on atom
connectivity, not Drude connectivity) are excluded and electrostatics calculated
via Thole. You don't have any bonds, so the choice here is not exactly clear
and I don't want to pre-judge without knowing what the force field is or how it
should be expected to behave.
3. Playing with the "a" factor of the Thole scheme resulted in more
pronounced changes in the contribution from polarization but I still
As it should; the value of a should be the sum of the two atomic Thole factors,
or 2.6, whichever your force field uses.
see too strong Coulombic interactions. Omitting shell particles and
thus polarization do scale Coulombics down by a factor of 100 or 1000.
I guess that using [polarization] all dipoles interact with all the
others (although no idea how dipoles interact through walls of the cell).
I imagine that in the [thole_polarization] case only those dipole pairs
will interact that I have mindlessly selected.
In contrast with my expectation I noticed an order of magnitude
greater Thole pol. values than Polarization values in the simple
pol. case. (For your information, I have ca. 2000 atoms + 1000 shell
particles in a box of ca. 3x3x3 nm. In case of the Thole scheme
I have ca. 1e5 pcs. of dipole pairs with a 1 nm radius for inclusion
while ca. 15000 for a radius of 0.5 nm.)
Sounds like it could be incorrect forces, but without seeing the Thole section
of your topology, I can't say for sure.
0.5 - 1.0 nm sounds like far too large of a radius for Thole interactions.
-Justin
The total potential is almost a pure Coulombic one and is too large.
Do you have any hint on what could go wrong?
Thanks for your attention.
With best regards,
toma
On Fri, Jul 25, 2014 at 9:31 PM, Tamas Karpati <tkarp...@gmail.com> wrote:
Dear Justin,
Thank you for the valuable information. I'm starting experimenting with it.
Have a nice weekend,
toma
On Fri, Jul 25, 2014 at 7:53 PM, Justin Lemkul <jalem...@vt.edu> wrote:
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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==================================================
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Ruth L. Kirschstein NRSA Postdoctoral Fellow
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Justin A. Lemkul, Ph.D.
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Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201
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http://mackerell.umaryland.edu/~jalemkul
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