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

Tamas Karpati tkarpati at gmail.com
Fri Jul 25 18:40:16 CEST 2014

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.

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).

I appreciate your help so much.

With regards,

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