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

[Tamas Karpati]

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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