Integrators¶
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class
Integrator¶ The
Integratorare a wrapper around the integrators provided by OpenMM and have to be attached to theSettingswhen setting up a simulation. They define the algorithm used to integrate the equations of motion of the system.
Verlet Dynamics¶
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class
VerletIntegrator(step_size)¶ Implementation of Verlet dynamics
Parameters: step_size ( float) – Defining timestep in ps
Langevin Dynamics¶
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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
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GetTemperature()¶ Returns: float- the temperature in K
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SetTemperature(temperature)¶ Parameters: temperature ( float) – Temperature in K
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GetFriction()¶ Returns: float- the friction in 1/ps
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SetFriction(friction)¶ Parameters: friction ( float) – Friction in 1/ps
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GetRandomNumberSeed()¶ Returns: int
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SetRandomNumberSeed(seed)¶ Parameters: seed ( int) – Random number seed
- temperature (
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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
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GetTemperature()¶ Returns: float- the temperature in K
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SetTemperature(temperature)¶ Parameters: temperature ( float) – Temperature in K
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GetFriction()¶ Returns: float- the friction in 1/ps
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SetFriction(friction)¶ Parameters: friction ( float) – Friction in 1/ps
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GetRandomNumberSeed()¶ Returns: int
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SetRandomNumberSeed(seed)¶ Parameters: seed ( int) – Random number seed
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GetErrorTolerance()¶ Returns: float
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SetErrorTolerance(tol)¶ Parameters: tol ( float) – Error tolerance
- temperature (
Brownian Dynamics¶
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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.
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GetTemperature()¶ Returns: float- the temperature in K
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SetTemperature(temperature)¶ Parameters: temperature ( float) – Temperature in K
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GetFriction()¶ Returns: float- the friction in 1/ps
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SetFriction(friction)¶ Parameters: friction ( float) – Friction in 1/ps
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GetRandomNumberSeed()¶ Returns: int
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SetRandomNumberSeed(seed)¶ Parameters: seed ( int) – Random number seed
- temperature (