Integrators

class Integrator

The Integrator are a wrapper around the integrators provided by OpenMM and have to be attached to the Settings when setting up a simulation. They define the algorithm used to integrate the equations of motion of the system.

Verlet Dynamics

class VerletIntegrator(step_size)

Implementation of Verlet dynamics

Parameters:

step_size (float) – Defining timestep in ps

class VariableVerletIntegrator(error_tol)

Implementation of Verlet dynamics with variable time steps

Parameters:

error_tol (float) – Error tolerance

GetErrorTolerance()

Returns:

float

SetErrorTolerance(tol)

Parameters:

tol (float) – Error tolerance

Langevin Dynamics

class LangevinIntegrator(temperature, friction_coeff, step_size)

Implementation of the Langevin dynamics

Parameters:

• temperature (float) – Temperature of heat bath in K

• friction_coeff (float) – Friction coefficient coupling the system to the heat bath in 1/ps

• step_size (float) – Defining timestep in ps

GetTemperature()

Returns:

float - the temperature in K

SetTemperature(temperature)

Parameters:

temperature (float) – Temperature in K

GetFriction()

Returns:

float - the friction in 1/ps

SetFriction(friction)

Parameters:

friction (float) – Friction in 1/ps

GetRandomNumberSeed()

Returns:

int

SetRandomNumberSeed(seed)

Parameters:

seed (int) – Random number seed

class VariableLangevinIntegrator(temperature, friction_coeff, error_tol)

Implementation of Langevin dynamics with variable time steps

Parameters:

• temperature (float) – Temperature of heat bath in K

• friction_coeff (float) – Friction coefficient coupling the system to the heat bath in 1/ps

• error_tol – Error tolerance

GetTemperature()

Returns:

float - the temperature in K

SetTemperature(temperature)

Parameters:

temperature (float) – Temperature in K

GetFriction()

Returns:

float - the friction in 1/ps

SetFriction(friction)

Parameters:

friction (float) – Friction in 1/ps

GetRandomNumberSeed()

Returns:

int

SetRandomNumberSeed(seed)

Parameters:

seed (int) – Random number seed

GetErrorTolerance()

Returns:

float

SetErrorTolerance(tol)

Parameters:

tol (float) – Error tolerance

Brownian Dynamics

class BrownianIntegrator(temperature, friction_coeff, step_size)

Implementation of Brownian dynamics

Parameters:

• temperature (float) – Temperature of heat bath in K

• friction_coeff (float) – Friction coefficient coupling the system to the heat bath in 1/ps

• step_size (float) – Defining timestep in ps.

GetTemperature()

Returns:

float - the temperature in K

SetTemperature(temperature)

Parameters:

temperature (float) – Temperature in K

GetFriction()

Returns:

float - the friction in 1/ps

SetFriction(friction)

Parameters:

friction (float) – Friction in 1/ps

GetRandomNumberSeed()

Returns:

int

SetRandomNumberSeed(seed)

Parameters:

seed (int) – Random number seed