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