CHARMM Angle Style

Overview

Define a three-body potential energy function corresponding to the CHARMM angle style

\[U_{ijk} = \frac{1}{2}K(\theta - \theta_0)^2 + \frac{1}{2}K_{\text{ub}}(r-r_{\text{ub}})^2,\]

where \(K, \theta_0, K_{\text{ub}}, r_{\text{ub}}\) are coefficients that must be set to define the interaction between atoms \(i, j, k\) .

Angles and types can be defined directly within the python input script, read from a LAMMPS data file (using the LAMMPS reader utility), read from a NAMD input file (using the NAMD reader utility) or read from a restart file.

Python Member Functions

Setting angle types and angles from within the Python environment is done with simple invocations. Parameters with = may be given in any order and are also optionally specified. For example, if an existing angle type has already been set, it is unneccessary to specify its parameters again when creating an angle for three atoms.

setAngleTypeCoefs(k=...,theta0=...,kub=...,rub=...,type=...)
createAngle(a,b,c,k=...,theta0=...,kub=...,rub=...,type=...)

Arguments

a,b,c

Indices for atoms for which the angle is defined.

k

Spring constant coefficient for harmonic interaction.

theta0

Equilbrium angle for harmonic angle interaction (specified in radians).

kub

Urey-Bradley coefficient for 1-3 interaction.

rub

Equilibrium Urey-Bradley separation distance.

type

Integer indicating the angle type assignment

Examples

Adding the fix

#Add Fix for CHARMM angle style
anglePot = FixAngleCHARMM(state,'anglePot')

Setting angle type coefficients in python

#Setting angle types
anglePot.setAngleTypeCoefs(k=100.0,theta0=2*pi/3.,type=0)

Defining an angle type in python

#Creating an angle between atoms 1,2,3
a=1     # index for atom 1
b=2     # index for atom 2
c=3     # index for atom 3
d=3     # index for atom 4
anglePot.createAngle(a,b,c,type=0)
# create angle and implicitly create type
anglePot.createAngle(b,c,d,k=80.0,theta0=pi*100./180.,kub=10.0,rub=1.0,type=1)

Activating the fix

#Activate fix
state.activateFix(anglePot)

LAMMPS data file parameter order

angle_coeff type k theta0 kub rub