[gmx-users] How to extend the force field by polariation parameters

[Zuzana Benkova]

Dear Justin,

thank you for your answer. 
As I noticed, there is a model of Drude oscillators (shells) used in GROMACS to represent the polarization of atoms. However, there exists model of rigid rod dipole moment which, instead of oscillating distance between the core nucleus and the auxiliary particle, assumes rigid length between them.
In this model, the virtual site has no van der Waals interactions, while it has a charge q and a mass m. Unlike the Drude oscillator, this rod a has a finite dipole moment = charge x length. Thus, it requires an orientational averaging (i.e., T > 0) to produce physically meaningful results. The rod involves three parameters: length, charge, and mass.The polarizability is (charge x length)^2/(3kbT) and the intrinsic time scale is given by (2kbT/(length^2 x mass)^0.5. Such a model has been already used. The authors carried out the simulations for graphene (GRAPPA FF) using GROMACS (Nanoscale, 2014, 6, 5438). 
I just wonder if I could adopt this model without changes in code by using virtual interaction sites.

Thanks.

Greetings

Zuzana




----- Original Message -----
From: "Justin Lemkul" <jalemkul at vt.edu>
To: "gmx-users" <gmx-users at gromacs.org>
Sent: Friday, April 10, 2020 3:05:47 PM
Subject: Re: [gmx-users] How to extend the force field by polariation parameters

On 4/9/20 8:06 PM, Zuzana Benkova wrote:
> Dear GROMACS users,
>
> I am trying to extend the CHARMM force field of graphene by polarization of carbon atoms. I need  to use the rigid rod dipole model, with a dipole on each
> carbon atom, with length of 0.7 A° combined with a charge of 0.1 e, which yields a polarization of 0.910 A°^3 (GRAPPA).
>
> Can you suggest me some literature where I can get some idea how to do it? In GROMACS manual, I have found Chapter  4.4. related to the polarization but it contains only information on  simple polarization, water polarization and Thole polarization and doesn't provide some hint how to extend a given force field.

If your model has a fixed length between the core nucleus and the 
auxiliary particle, it's not a "polarizable" model because the dipoles 
cannot relax/change length, therefore nothing related to polarization 
options is relevant to you. You will have particles that are at a fixed 
distance from their nucleus (e.g. via [constraints])

-Justin

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