dipole moment / polarizability from AMOEBA

[Daniel Konstantinovsky]

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

[Peter Eastman]

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.

[Daniel Konstantinovsky]

Thank you! I was also wondering if AMOEBA outputs atomic polarizability tensors as well as dipoles, and are those constants in the AMOEBA model?

[Peter Eastman]

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.

[Daniel Konstantinovsky]

Got it, thanks!