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
dipole moment / polarizability from AMOEBA
- Daniel Konstantinovsky
- Posts: 77
- Joined: Tue Jun 11, 2019 12:21 pm
- Peter Eastman
- Posts: 2588
- Joined: Thu Aug 09, 2007 1:25 pm
Re: dipole moment / polarizability from AMOEBA
Yes, I think you can do that. First find the AmoebaMultipoleForce in your System:
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.
Code: Select all
for force in system.getForces():
if isinstance(force, AmoebaMultipoleForce):
...
- Daniel Konstantinovsky
- Posts: 77
- Joined: Tue Jun 11, 2019 12:21 pm
Re: dipole moment / polarizability from AMOEBA
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
- Posts: 2588
- Joined: Thu Aug 09, 2007 1:25 pm
Re: dipole moment / polarizability from AMOEBA
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
- Posts: 77
- Joined: Tue Jun 11, 2019 12:21 pm
Re: dipole moment / polarizability from AMOEBA
Got it, thanks!