Package ffx.algorithms.thermodynamics

Class RepExOST

java.lang.Object

ffx.algorithms.thermodynamics.RepExOST

public class RepExOST
extends Object

An implementation of RepEx between Orthogonal Space Tempering potentials.

Since:

1.0

Author:

Jacob Litman, Michael J. Schnieders

Method Summary

Modifier and Type	Method	Description
OrthogonalSpaceTempering	getOST()
void	mainLoop(long numTimesteps, boolean equilibrate)	Executes the main loop of RepExOST.
static RepExOST	repexMC(OrthogonalSpaceTempering orthogonalSpaceTempering, MonteCarloOST monteCarloOST, DynamicsOptions dynamicsOptions, OSTOptions ostOptions, org.apache.commons.configuration2.CompositeConfiguration compositeConfiguration, String fileType, boolean twoStep, double repexInterval)	Construct a RepExOST for Monte Carlo orthogonal space tempering.
static RepExOST	repexMD(OrthogonalSpaceTempering orthogonalSpaceTempering, MolecularDynamics molecularDynamics, DynamicsOptions dynamicsOptions, OSTOptions ostOptions, org.apache.commons.configuration2.CompositeConfiguration compositeConfiguration, String fileType, double repexInterval)	Construct a RepExOST for Molecular Dynamics orthogonal space tempering.

Methods inherited from class java.lang.Object

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

Method Details

repexMC

public static RepExOST repexMC(OrthogonalSpaceTempering orthogonalSpaceTempering,
 MonteCarloOST monteCarloOST,
 DynamicsOptions dynamicsOptions,
 OSTOptions ostOptions,
 org.apache.commons.configuration2.CompositeConfiguration compositeConfiguration,
 String fileType,
 boolean twoStep,
 double repexInterval)
                        throws IOException

Construct a RepExOST for Monte Carlo orthogonal space tempering.

Parameters:

orthogonalSpaceTempering - An OrthogonalSpaceTempering for each RepEx rung.

monteCarloOST - A MonteCarloOST for each RepEx rung

dynamicsOptions - DynamicsOptions to apply universally.

ostOptions - OST options to apply.

compositeConfiguration - CompositeConfiguration properties to use.

fileType - File type to save to.

twoStep - Whether to use the 2-step MC algorithm (instead of the 1-step).

repexInterval - Interval in psec between RepEx attempts.

Returns:

A RepExOST.

Throws:

IOException - if one occurs constructing RepExOST.

repexMD

public static RepExOST repexMD(OrthogonalSpaceTempering orthogonalSpaceTempering,
 MolecularDynamics molecularDynamics,
 DynamicsOptions dynamicsOptions,
 OSTOptions ostOptions,
 org.apache.commons.configuration2.CompositeConfiguration compositeConfiguration,
 String fileType,
 double repexInterval)
                        throws IOException

Construct a RepExOST for Molecular Dynamics orthogonal space tempering.

Parameters:

orthogonalSpaceTempering - An OrthogonalSpaceTempering for each RepEx rung.

molecularDynamics - A MolecularDynamics for each RepEx rung.

dynamicsOptions - DynamicsOptions to apply universally.

ostOptions - OST options to apply.

compositeConfiguration - CompositeConfiguration properties to use.

fileType - File type to save to.

repexInterval - Interval in psec between RepEx attempts.

Returns:

A RepExOST.

Throws:

IOException - if one occurs constructing RepExOST.

getOST

public OrthogonalSpaceTempering getOST()

mainLoop

public void mainLoop(long numTimesteps,
 boolean equilibrate)
              throws IOException

Executes the main loop of RepExOST.

Parameters:

numTimesteps - Number of times steps.

equilibrate - If true, perform equilibration.

Throws:

IOException - Possible from Parallel Java.