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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

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