Polarization¶
Polarization can be treated by GROMACS by attaching shell (Drude) particles to atoms and/or virtual sites. The energy of the shell particle is then minimized at each time step in order to remain on the Born-Oppenheimer surface.
Simple polarization¶
This is implemented as a harmonic potential with equilibrium distance 0.
The input given in the topology file is the polarizability
[ polarization ]
; Atom i j type alpha
1 2 1 0.001
in this case the polarizability volume is 0.001 nm
where
Anharmonic polarization¶
For the development of the Drude force field by Roux and McKerell 93 it was found that some particles can overpolarize and this was fixed by introducing a higher order term in the polarization energy:
where
[ polarization ]
;Atom i j type alpha (nm^3) delta khyp
1 2 2 0.001786 0.02 16.736e8
The above force constant
Water polarization¶
A special potential for water that allows anisotropic polarization of a single shell particle 45.
Thole polarization¶
Based on early work by Thole 95, Roux and coworkers
have implemented potentials for molecules like
ethanol 96, 98.
Within such molecules, there are intra-molecular interactions between
shell particles, however these must be screened because full Coulomb
would be too strong. The potential between two shell particles
Note that there is a sign error in Equation 1 of Noskov et al. 98:
where