[gmx-users] hints for core/shell optimization?

Tamas Karpati tkarpati at gmail.com
Tue Jul 29 15:33:39 CEST 2014

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?

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?

3. Playing with the "a" factor of the Thole scheme resulted in more
pronounced changes in the contribution from polarization but I still
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.)

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,

On Fri, Jul 25, 2014 at 9:31 PM, Tamas Karpati <tkarpati at 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 <jalemkul at 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
>> --
>> ==================================================
>> Justin A. Lemkul, Ph.D.
>> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>> Department of Pharmaceutical Sciences
>> School of Pharmacy
>> Health Sciences Facility II, Room 601
>> University of Maryland, Baltimore
>> 20 Penn St.
>> Baltimore, MD 21201
>> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
>> http://mackerell.umaryland.edu/~jalemkul
>> ==================================================
>> --
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