Package ffx.openmm

Class BrownianIntegrator

java.lang.Object

ffx.openmm.Integrator

ffx.openmm.BrownianIntegrator

public class BrownianIntegrator
extends Integrator

This is an Integrator which simulates a System using Brownian dynamics.

Field Summary

Fields inherited from class ffx.openmm.Integrator

pointer

Constructor Summary

Constructors

Constructor	Description
BrownianIntegrator(double temperature, double frictionCoeff, double stepSize)	Create a BrownianIntegrator.

Method Summary

Modifier and Type	Method	Description
void	destroy()	Destroy the integrator.
double	getFriction()	Get the friction coefficient which determines how strongly the system is coupled to the heat bath (in inverse ps).
int	getRandomNumberSeed()	Get the random number seed.
double	getTemperature()	Get the temperature of the heat bath (in Kelvin).
void	setFriction(double coeff)	Set the friction coefficient which determines how strongly the system is coupled to the heat bath (in inverse 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.

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

BrownianIntegrator

public BrownianIntegrator(double temperature,
 double frictionCoeff,
 double stepSize)

Create a BrownianIntegrator.

Parameters:

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

frictionCoeff - the friction coefficient which couples the system to the heat bath, measured in 1/ps

stepSize - the step size with which to integrate the system (in picoseconds)

Method Details

destroy

public void destroy()

Destroy the integrator.

Specified by:

destroy in class Integrator

getFriction

public double getFriction()

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

Returns:

the friction coefficient, measured in 1/ps

getRandomNumberSeed

public int getRandomNumberSeed()

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

getTemperature

public double getTemperature()

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

Returns:

the temperature of the heat bath (in Kelvin).

setFriction

public void setFriction(double coeff)

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

Parameters:

coeff - the friction coefficient, measured in 1/ps

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 forces 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.

setTemperature

public void setTemperature(double temp)

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

Parameters:

temp - the temperature of the heat bath, measured in Kelvin.

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