[gmx-users] Shell (Drude) model for polarization in GROMACS

[Justin Lemkul]

On 7/3/18 6:52 PM, Eric Smoll wrote:
> Justin,
>
> Thanks again for the response and the guidance.  Your 2015 JCC paper on the
> subject was very helpful.
>
> Your code uses a different thole_polarization format.  Currently, Gromacs
> uses the following format
> [ thole_polarization ]
> ;   i   j   k   l   function-number  thole-a-parameter   alpha_ij   alpha_kl
>
> Your code seems to use
> [ thole_polarization ]
> ;   i   j   k   l   function-number   alpha_ij   alpha_kl
> thole-a-parameter-1   thole-a-parameter-2
>
> If I would use 2.6 in the current Gromacs thole_polarization format, what
> would I use in your thole_polarization format?

1.3 for both atoms to get 1.3 + 1.3 = 2.6.  Thole's magic number quickly 
breaks down for complicated molecules, so our convention is that it is a 
per-atom value that is summed to give a new value of "a" per pair, e.g. 
a_i + a_j = a_total.

-Justin

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Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

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