Package ffx.algorithms.dynamics

Class ReplicaExchange

java.lang.Object

ffx.algorithms.dynamics.ReplicaExchange

All Implemented Interfaces:

Terminatable

public class ReplicaExchange
extends Object
implements Terminatable

The ReplicaExchange implements temperature and lambda replica exchange methods.

Since:

1.0

Author:

Timothy D. Fenn and Michael J. Schnieders

Constructor Summary

Constructors

Constructor	Description
ReplicaExchange(MolecularDynamics molecularDynamics, AlgorithmListener listener, double temperature, double exponent, boolean monteCarlo)	ReplicaExchange constructor.

Method Summary

Modifier and Type	Method	Description
void	sample(int cycles, long nSteps, double timeStep, double printInterval, double saveInterval)	Sample.
void	setExponentialTemperatureLadder(double lowTemperature, double exponent)	setExponentialTemperatureLadder.
void	setTemperatures(double[] temperatures)	Setter for the field temperatures.
void	terminate()	This should be implemented as a blocking interrupt; when the method returns the Terminatable algorithm has reached a clean termination point.

Methods inherited from class java.lang.Object

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

Constructor Details

ReplicaExchange

public ReplicaExchange(MolecularDynamics molecularDynamics,
 AlgorithmListener listener,
 double temperature,
 double exponent,
 boolean monteCarlo)

ReplicaExchange constructor.

Parameters:

molecularDynamics - The MolecularDynamics instance.

listener - A listener for algorithm events.

temperature - The temperature (K).

exponent - a double to set temperature ladder.

Method Details

sample

public void sample(int cycles,
 long nSteps,
 double timeStep,
 double printInterval,
 double saveInterval)

Sample.

Parameters:

cycles - The number of cycles to sample.

nSteps - The number of steps per cycle.

timeStep - The time step (fsec).

printInterval - The interval (in steps) to print current status.

saveInterval - The interval (in steps) to save a snapshot.

setExponentialTemperatureLadder

public void setExponentialTemperatureLadder(double lowTemperature,
 double exponent)

setExponentialTemperatureLadder.

Parameters:

lowTemperature - a double.

exponent - a double.

setTemperatures

public void setTemperatures(double[] temperatures)

Setter for the field temperatures.

Parameters:

temperatures - The temperatures for each replica.

terminate

public void terminate()

This should be implemented as a blocking interrupt; when the method returns the Terminatable algorithm has reached a clean termination point. For example, between minimize or molecular dynamics steps.

This should be implemented as a blocking interrupt; when the method returns the Terminatable algorithm has reached a clean termination point. For example, between minimize or molecular dynamics steps.

Specified by:

terminate in interface Terminatable