"""A module for defining the TIP3P-FB forcefield
This definition of the TIP3P-FB forcefield includes bond and bond angle
strengths as these are needed for to create the required HarmonicPotentials. As
a result, they can be used for simulating a flexible water molecule. However,
TIP3P-FB itself is a rigid model, and in order to replicate this a constraint
algorithm should be used for all Bond and BondAngle objects.
Parameters (excluding bond strengths) are from:
Building Force Fields: An Automatic, Systematic, and Reproducible Approach
Lee-Ping Wang, Todd J. Martinez, and Vijay S. Pande
J. Phys. Chem. Lett. 2014, 5, 11, 1885–1891
The strengths provided are the same as those used for TIP3P, from:
https://lammps.sandia.gov/doc/Howto_tip3p.html
having converted from their units of kcal to our kJ.
Note that different values for bond strengths are given in the OPLSAA data
file, namely 2510.4 and 313.8 respectively."""
from MDMC.MD.force_fields.ff import WaterModel
from MDMC.MD.interaction_functions import (Coulomb, HarmonicPotential,
LennardJones)
from MDMC.MD.interactions import Bond, BondAngle, Dispersion, Coulombic
[docs]
class TIP3PFB(WaterModel):
"""
TIP3P-FB force field - LJ, Coulombic, fixed bond lengths and angles
"""
n_body = 3
@property
def interaction_dictionary(self):
# Parameters from:
# Building Force Fields: An Automatic, Systematic, and Reproducible
# Approach
# Lee-Ping Wang, Todd J. Martinez, and Vijay S. Pande
# J. Phys. Chem. Lett. 2014, 5, 11, 1885–1891
# Charge Parameters
q_O = -0.84844 # e
q_H = abs(q_O/2) # e
# LJ Parameters
sigma = 3.1780 # Ang
epsilon = 0.65214 # kJ mol^-1
# Bond Parameters
r_OH = 1.0118 # Ang
f_OH = 1882.8 # kJ mol^-1 Ang^-2
# Bond Angle Parameters
a_HOH = 108.15 # deg
f_HOH = 230.12 # kJ mol^-1 rad^-2
return {
(Coulombic, ('O',)): Coulomb(q_O),
(Coulombic, ('H',)): Coulomb(q_H),
(Dispersion, ('O', 'O')): LennardJones(epsilon, sigma),
(Bond,
('H', 'O')): HarmonicPotential(r_OH, f_OH, interaction_type='bond'),
(BondAngle,
('H', 'O', 'H')): HarmonicPotential(a_HOH, f_HOH,
interaction_type='angle')}