On Sun, Nov 12, 2023, Gillispie, Nathan via AMBER wrote:
>
>I'm an undergraduate researcher and a relatively new Amber user. I
>added polarizability to my calculations a few months ago...
It's not clear what you really did here. Did you use the "ff02" force
field, described in Seciton 3.12.4 of the Reference manual? Or are you
using the polarizable Gaussian multipole (pGM) model described in Section
21.8?
>First, how do Amber's polarizability forces work? I'm aware of the Epol
>term that's added to the basic potential, but how is that turned into a
>force on the atoms? Is it the force due to two electric dipoles along with
>dipole-monopole interactions? I assume this a point induced dipole model,
>but I thought there were problems with this model which cause the dipoles
>to blow up in some cases.
The ff02 force field indeed uses point dipoles, which damping terms to avoid
"polarizability catastrophes". The pGM model has polarizable Gaussians
which should avoid such problems. Details would require careful reading
of the relevant papers -- it's not really easy to answer in an email
(especially since I am not the right person to do that anyway.)
Turning these electrostatic interactions into forces is basically an
application of differentiation. This is in priciple straightforward, but in
practice leads to rather complex expressions.
>Second, I have access to Gaussian which allows me to determine the
>isotropic polarizabilities for molecules. Is this useful in any way, and
>more generally, are experimental polarizabilities useful in my case?
It sounds like you want to parametrize your own polarizable force fields,
e.g for non-proteins. Is that correct? The approach really depends on the
answer to my first question, above.
...hope this helps (some)....dac
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Received on Mon Nov 13 2023 - 09:00:02 PST
