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

[Tamas Karpati]

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,
  toma


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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