Package ffx.algorithms.mc

Class RosenbluthOBMC

java.lang.Object

ffx.algorithms.mc.RosenbluthOBMC

All Implemented Interfaces:

MonteCarloListener

public class RosenbluthOBMC
extends Object
implements MonteCarloListener

Orientational Biased Monte Carlo (as applied to chi0 torsion of peptide side-chains).

As described by Frenkel/Smit in "Understanding Molecular Simulation" Chapter 13.1.2. This uses the "orientational biasing" method to select chi[0] moves that are frequently accepted.

Author:

Stephen D. LuCore

Constructor Summary

Constructors

Constructor	Description
RosenbluthOBMC(MolecularAssembly molecularAssembly, ForceFieldEnergy forceFieldEnergy, Thermostat thermostat, List<Residue> targets, int mcFrequency, int trialSetSize)	RRMC constructor.
RosenbluthOBMC(MolecularAssembly molecularAssembly, ForceFieldEnergy forceFieldEnergy, Thermostat thermostat, List<Residue> targets, int mcFrequency, int trialSetSize, boolean writeSnapshots)	Constructor for RosenbluthOBMC.

Method Summary

Modifier and Type	Method	Description
boolean	mcUpdate(double temperature)	After a successful step or interval of an algorithm, this method of the listener will be called.

Methods inherited from class java.lang.Object

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

Constructor Details

RosenbluthOBMC

public RosenbluthOBMC(MolecularAssembly molecularAssembly,
 ForceFieldEnergy forceFieldEnergy,
 Thermostat thermostat,
 List<Residue> targets,
 int mcFrequency,
 int trialSetSize)

RRMC constructor.

Parameters:

molecularAssembly - a MolecularAssembly object.

forceFieldEnergy - a ForceFieldEnergy object.

thermostat - a Thermostat object.

targets - Residues to undergo RRMC.

mcFrequency - Number of MD steps between RRMC proposals.

trialSetSize - Larger values cost more but increase acceptance.

RosenbluthOBMC

public RosenbluthOBMC(MolecularAssembly molecularAssembly,
 ForceFieldEnergy forceFieldEnergy,
 Thermostat thermostat,
 List<Residue> targets,
 int mcFrequency,
 int trialSetSize,
 boolean writeSnapshots)

Constructor for RosenbluthOBMC.

Parameters:

molecularAssembly - a MolecularAssembly object.

forceFieldEnergy - a ForceFieldEnergy object.

thermostat - a Thermostat object.

targets - a List object.

mcFrequency - a int.

trialSetSize - a int.

writeSnapshots - a boolean.

Method Details

mcUpdate

public boolean mcUpdate(double temperature)

After a successful step or interval of an algorithm, this method of the listener will be called.

Temperature argument is necessary since Potentials package cannot import Thermostat/MD.

Specified by:

mcUpdate in interface MonteCarloListener

Parameters:

temperature - The Metropolis Monte Carlo temperature.

Returns:

A return of true indicates the algorithm continues.