Package ffx.algorithms.dynamics

Class MolecularDynamicsOpenMM

java.lang.Object

ffx.algorithms.dynamics.MolecularDynamics

ffx.algorithms.dynamics.MolecularDynamicsOpenMM

All Implemented Interfaces:

Terminatable, Runnable

public class MolecularDynamicsOpenMM
extends MolecularDynamics

Runs Molecular Dynamics using OpenMM implementation

Author:

Michael J. Schnieders

Field Summary

Fields inherited from class ffx.algorithms.dynamics.MolecularDynamics

algorithmListener, automaticWriteouts, done, dt, fileType, initialState, initVelocities, logFrequency, molecularAssembly, restartFrequency, restartInterval, state, totalSimTime, trajectoryFrequency

Constructor Summary

Constructors

Constructor	Description
MolecularDynamicsOpenMM(MolecularAssembly assembly, Potential potential, AlgorithmListener listener, ThermostatEnum thermostat, IntegratorEnum integrator)	Constructs an MolecularDynamicsOpenMM object, to perform molecular dynamics using native OpenMM routines, avoiding the cost of communicating coordinates, gradients, and energies back and forth across the PCI bus.

Method Summary

Modifier and Type	Method	Description
protected void	appendSnapshot(String[] extraLines)	Append a snapshot to the trajectory file.
void	dynamic(long numSteps, double timeStep, double printInterval, double saveInterval, double temperature, boolean initVelocities, File dyn)	Blocking molecular dynamics.
int	getIntervalSteps()	getIntervalSteps.
double	getTimeStep()	getTimeStep.
void	init(long numSteps, double timeStep, double loggingInterval, double trajectoryInterval, String fileType, double restartInterval, double temperature, boolean initVelocities, File dyn)	init
void	revertState()	Revert the state of the MolecularDynamics instance to the stored MDState.
void	setFileType(String fileType)	Method to set file type from groovy scripts.
void	setIntervalSteps(int intervalSteps)	Setter for the field intervalSteps.
void	setObtainVelAcc(boolean obtainVA)	Sets whether to obtain all variables (velocities, gradients) from OpenMM, or just positions and energies.
void	writeRestart()	Write out a restart file.

Methods inherited from class ffx.algorithms.dynamics.MolecularDynamics

addAssembly, attachExtendedSystem, dynamic, dynamicsFactory, dynamicsFactory, getAssemblyArray, getCoordinates, getDynFile, getInitialKineticEnergy, getInitialPotentialEnergy, getInitialTemperature, getInitialTotalEnergy, getKineticEnergy, getPotentialEnergy, getTemperature, getThermostat, getTotalEnergy, getVerbosityLevel, init, logThermoForTime, run, setArchiveFiles, setAutomaticWriteouts, setCoordinates, setFallbackDynFile, setRestartFrequency, setThermostat, setVerbosityLevel, storeState, terminate, writeFilesForStep, writeFilesForStep

Methods inherited from class java.lang.Object

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

Constructor Details

MolecularDynamicsOpenMM

public MolecularDynamicsOpenMM(MolecularAssembly assembly,
 Potential potential,
 AlgorithmListener listener,
 ThermostatEnum thermostat,
 IntegratorEnum integrator)

Constructs an MolecularDynamicsOpenMM object, to perform molecular dynamics using native OpenMM routines, avoiding the cost of communicating coordinates, gradients, and energies back and forth across the PCI bus.

Parameters:

assembly - MolecularAssembly to operate on

potential - Either a ForceFieldEnergyOpenMM, or a Barostat.

listener - a AlgorithmListener object.

thermostat - May have to be slightly modified for native OpenMM routines

integrator - May have to be slightly modified for native OpenMM routines

Method Details

dynamic

public void dynamic(long numSteps,
 double timeStep,
 double printInterval,
 double saveInterval,
 double temperature,
 boolean initVelocities,
 File dyn)

Blocking molecular dynamics. When this method returns, the MD run is done.

Execute numSteps of dynamics using the provided timeStep and temperature. The printInterval and saveInterval control logging the state of the system to the console and writing a restart file, respectively. If the dyn File is not null, the simulation will be initialized from the contents. If the iniVelocities is true, the velocities will be initialized from a Maxwell Boltzmann distribution.

Overrides:

dynamic in class MolecularDynamics

Parameters:

numSteps - Number of MD steps

timeStep - Time step (fsec)

printInterval - Interval between printing/logging information in picoseconds.

saveInterval - Interval between adding a frame to the trajectory file in picoseconds.

temperature - Temperature in Kelvins.

initVelocities - Initialize new velocities from a Maxwell-Boltzmann distribution.

dyn - A File object to write the restart file to.

getIntervalSteps

public int getIntervalSteps()

getIntervalSteps.

Overrides:

getIntervalSteps in class MolecularDynamics

Returns:

Always 1 for this implementation.

setIntervalSteps

public void setIntervalSteps(int intervalSteps)

Setter for the field intervalSteps.

Overrides:

setIntervalSteps in class MolecularDynamics

Parameters:

intervalSteps - The number of interval steps.

getTimeStep

public double getTimeStep()

getTimeStep.

Overrides:

getTimeStep in class MolecularDynamics

Returns:

Time step in picoseconds.

init

public void init(long numSteps,
 double timeStep,
 double loggingInterval,
 double trajectoryInterval,
 String fileType,
 double restartInterval,
 double temperature,
 boolean initVelocities,
 File dyn)

init

Overrides:

init in class MolecularDynamics

Parameters:

numSteps - Number of MD steps

timeStep - Time step in femtoseconds

loggingInterval - Interval between printing/logging information in picoseconds.

trajectoryInterval - Interval between adding a frame to the trajectory file in picoseconds.

fileType - XYZ or ARC to save to .arc, PDB for .pdb files

restartInterval - Interval between writing new restart files in picoseconds.

temperature - Temperature in Kelvins.

initVelocities - Initialize new velocities from a Maxwell-Boltzmann distribution.

dyn - A File object to write the restart file to.

revertState

public void revertState()
                 throws Exception

Description copied from class: MolecularDynamics

Revert the state of the MolecularDynamics instance to the stored MDState.

Overrides:

revertState in class MolecularDynamics

Throws:

Exception - is thrown if the stored state is null.

setFileType

public void setFileType(String fileType)

Method to set file type from groovy scripts.

Overrides:

setFileType in class MolecularDynamics

Parameters:

fileType - the type of snapshot files to write.

setObtainVelAcc

public void setObtainVelAcc(boolean obtainVA)

Sets whether to obtain all variables (velocities, gradients) from OpenMM, or just positions and energies.

Overrides:

setObtainVelAcc in class MolecularDynamics

Parameters:

obtainVA - If true, obtain all variables from OpenMM each update.

writeRestart

public void writeRestart()

Description copied from class: MolecularDynamics

Write out a restart file.

Overrides:

writeRestart in class MolecularDynamics

appendSnapshot

protected void appendSnapshot(String[] extraLines)

Description copied from class: MolecularDynamics

Append a snapshot to the trajectory file.

Overrides:

appendSnapshot in class MolecularDynamics

Parameters:

extraLines - Strings of meta-data to include.