Package ffx.openmm

Class VariableLangevinIntegrator

java.lang.Object

ffx.openmm.Integrator

ffx.openmm.VariableLangevinIntegrator

public class VariableLangevinIntegrator
extends Integrator

This class implements a Langevin integrator with variable time stepping. The integrator automatically adjusts the step size to maintain a specified error tolerance, making it suitable for systems with widely varying time scales.

The variable step size algorithm monitors the local truncation error and adjusts the step size accordingly. This can lead to more efficient integration for systems where different parts evolve on different time scales, such as systems with both fast vibrations and slow conformational changes.

Field Summary

Fields inherited from class ffx.openmm.Integrator

pointer

Constructor Summary

Constructors

Constructor	Description
VariableLangevinIntegrator(double temperature, double frictionCoeff, double errorTol)	Create a VariableLangevinIntegrator.

Method Summary

Modifier and Type	Method	Description
void	destroy()	Destroy the integrator.
double	getErrorTolerance()	Get the error tolerance for adaptive step sizing.
double	getFriction()	Get the friction coefficient which determines how strongly the system is coupled to the heat bath (in 1/ps).
double	getMaximumStepSize()	Get the maximum step size the integrator is allowed to use (in ps).
int	getRandomNumberSeed()	Get the random number seed.
double	getTemperature()	Get the temperature of the heat bath (in Kelvin).
void	setErrorTolerance(double tol)	Set the error tolerance for adaptive step sizing.
void	setFriction(double coeff)	Set the friction coefficient which determines how strongly the system is coupled to the heat bath (in 1/ps).
void	setMaximumStepSize(double size)	Set the maximum step size the integrator is allowed to use (in ps).
void	setRandomNumberSeed(int seed)	Set the random number seed.
void	setTemperature(double temp)	Set the temperature of the heat bath (in Kelvin).
void	step(int steps)	Advance a simulation through time by taking a series of time steps.
void	stepTo(double time)	Advance the simulation by integrating until a specified time is reached.

Methods inherited from class ffx.openmm.Integrator

getConstraintTolerance, getIntegrationForceGroups, getPointer, getStepSize, setConstraintTolerance, setIntegrationForceGroups, setPointer, setStepSize

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Details

VariableLangevinIntegrator

public VariableLangevinIntegrator(double temperature,
 double frictionCoeff,
 double errorTol)

Create a VariableLangevinIntegrator.

Parameters:

temperature - The temperature of the heat bath (in Kelvin).

frictionCoeff - The friction coefficient which couples the system to the heat bath (in 1/ps).

errorTol - The error tolerance for adaptive step sizing.

Method Details

destroy

public void destroy()

Destroy the integrator.

Specified by:

destroy in class Integrator

getErrorTolerance

public double getErrorTolerance()

Get the error tolerance for adaptive step sizing.

Returns:

The error tolerance.

getFriction

public double getFriction()

Get the friction coefficient which determines how strongly the system is coupled to the heat bath (in 1/ps).

Returns:

The friction coefficient.

getMaximumStepSize

public double getMaximumStepSize()

Get the maximum step size the integrator is allowed to use (in ps).

Returns:

The maximum step size.

getRandomNumberSeed

public int getRandomNumberSeed()

Get the random number seed. See setRandomNumberSeed() for details.

Returns:

The random number seed.

getTemperature

public double getTemperature()

Get the temperature of the heat bath (in Kelvin).

Returns:

The temperature of the heat bath.

setErrorTolerance

public void setErrorTolerance(double tol)

Set the error tolerance for adaptive step sizing.

Parameters:

tol - The error tolerance.

setFriction

public void setFriction(double coeff)

Set the friction coefficient which determines how strongly the system is coupled to the heat bath (in 1/ps).

Parameters:

coeff - The friction coefficient.

setMaximumStepSize

public void setMaximumStepSize(double size)

Set the maximum step size the integrator is allowed to use (in ps).

Parameters:

size - The maximum step size.

setRandomNumberSeed

public void setRandomNumberSeed(int seed)

Set the random number seed. The precise meaning of this parameter is undefined, and is left up to each Platform to interpret in an appropriate way. It is guaranteed that if two simulations are run with different random number seeds, the sequence of random numbers will be different. On the other hand, no guarantees are made about the behavior of simulations that use the same seed. In particular, Platforms are permitted to use non-deterministic algorithms which produce different results on successive runs, even if those runs were initialized identically.

If seed is set to 0 (which is the default value assigned), a unique seed is chosen when a Context is created from this Force. This is done to ensure that each Context receives unique random seeds without you needing to set them explicitly.

Parameters:

seed - The random number seed.

setTemperature

public void setTemperature(double temp)

Set the temperature of the heat bath (in Kelvin).

Parameters:

temp - The temperature of the heat bath.

step

public void step(int steps)

Advance a simulation through time by taking a series of time steps.

Overrides:

step in class Integrator

Parameters:

steps - The number of time steps to take.

stepTo

public void stepTo(double time)

Advance the simulation by integrating until a specified time is reached.

Parameters:

time - The time to which the simulation should be advanced (in ps).