[AMBER] Polarizabilitiy Calculations

From: Gillispie, Nathan via AMBER <amber.ambermd.org>
Date: Sun, 12 Nov 2023 23:27:05 +0000

Hello Amber Users,

I'm an undergraduate researcher and a relatively new Amber user. I added polarizability to my calculations a few months ago and have been trying to find ways to get the most accurate polarizability values in my simulations. My question comes in a few parts.

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.

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? Since the Lennard-Jones potential models van Der Waals interactions, Amber is definitely including some polarizability effects which would lower the values put into the simulation. Polarizabilities of individual atoms in a molecule add together in a very non-linear way to get the total polarizability of the molecule. This leads me to believe you just have to make an educated guess on polarizability and hope the simulation is accurate. So lastly, is there any systematic way of determining what these values may be?

Thanks in advance,
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Received on Sun Nov 12 2023 - 15:30:02 PST
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