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dipole moment / polarizability from AMOEBA
Posted: Wed Sep 01, 2021 5:29 am
by dkonstan
Hi!
I'm exploring the possibility of using OpenMM and AMOEBA to calculate vibrational spectra of water. I was wondering how OpenMM can be used to extract the dipole and polarizability of atoms/molecules of interest from an AMOEBA simulation. I don't know if this is even possible but I thought I would ask.
Thank you!
Dan
Re: dipole moment / polarizability from AMOEBA
Posted: Wed Sep 01, 2021 9:47 am
by peastman
Yes, I think you can do that. First find the AmoebaMultipoleForce in your System:
Code: Select all
for force in system.getForces():
if isinstance(force, AmoebaMultipoleForce):
...
Then you can call methods on it to query dipole moments of atoms: getLabFramePermanentDipoles(), getInducedDipoles(), and getTotalDipoles(). See the documentation at
http://docs.openmm.org/latest/api-pytho ... ipoleForce.
Re: dipole moment / polarizability from AMOEBA
Posted: Wed Sep 01, 2021 10:48 am
by dkonstan
Thank you! I was also wondering if AMOEBA outputs atomic polarizability tensors as well as dipoles, and are those constants in the AMOEBA model?
Re: dipole moment / polarizability from AMOEBA
Posted: Wed Sep 01, 2021 10:53 am
by peastman
In AMOEBA, polarization is isotropic. The polarizability is just a single number for each atom. You can query it by calling getMultipoleParameters() on the AmobeMultipoleForce.
Re: dipole moment / polarizability from AMOEBA
Posted: Wed Sep 01, 2021 10:58 am
by dkonstan
Got it, thanks!