Package ffx.potential.openmm

Class OpenMMSystem

java.lang.Object

ffx.openmm.System

ffx.potential.openmm.OpenMMSystem

public class OpenMMSystem
extends System

Create and manage an OpenMM System.

The definition of a System involves four elements:

The particles and constraints are defined directly by the System object, while forces are defined by objects that extend the Force class. After creating a System, call addParticle() once for each particle, addConstraint() for each constraint, and addForce() for each Force.

In addition, particles may be designated as "virtual sites". These are particles whose positions are computed automatically based on the positions of other particles. To define a virtual site, call setVirtualSite(), passing in a VirtualSite object that defines the rules for computing its position.

Constructor Summary

Constructors

Constructor	Description
OpenMMSystem(OpenMMEnergy openMMEnergy)	OpenMMSystem constructor.

Method Summary

Modifier and Type	Method	Description
void	addAndersenThermostatForce(double targetTemp)	Add an Andersen thermostat to the system.
void	addAndersenThermostatForce(double targetTemp, double collisionFreq)	Add an Andersen thermostat to the system.
void	addCOMMRemoverForce()	Adds a force that removes center-of-mass motion.
void	addForces()	Add forces to the system.
void	addMonteCarloBarostatForce(double targetPressure, double targetTemp, int frequency)	Add a Monte Carlo Barostat to the system.
int	calculateDegreesOfFreedom()	Calculate the number of degrees of freedom.
void	free()	Destroy the system.
Crystal	getCrystal()	Get the Crystal instance.
ForceField	getForceField()	Get the ForceField in use.
int	getNumberOfVariables()	Get the number of variables.
double	getTemperature(double kineticEnergy)
boolean	hasAmoebaCavitationForce()
void	removeForce(Force force)	Remove a force from the OpenMM System.
void	setUpdateBondedTerms(boolean updateBondedTerms)
void	updateAtomMass()	This method sets the mass of inactive atoms to zero.
void	updateParameters(Atom[] atoms)	Update parameters if the Use flags and/or Lambda value has changed.

Methods inherited from class ffx.openmm.System

addConstraint, addForce, addParticle, destroy, getNumConstraints, getPointer, removeForce, setDefaultPeriodicBoxVectors, setParticleMass

Methods inherited from class java.lang.Object

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

Constructor Details

OpenMMSystem

public OpenMMSystem(OpenMMEnergy openMMEnergy)

OpenMMSystem constructor.

Parameters:

openMMEnergy - ForceFieldEnergyOpenMM instance.

Method Details

addForces

public void addForces()

Add forces to the system.

removeForce

public void removeForce(Force force)

Remove a force from the OpenMM System. The OpenMM memory associated with the removed Force object is deleted.

addAndersenThermostatForce

public void addAndersenThermostatForce(double targetTemp)

Add an Andersen thermostat to the system.

Parameters:

targetTemp - Target temperature in Kelvins.

addAndersenThermostatForce

public void addAndersenThermostatForce(double targetTemp,
 double collisionFreq)

Add an Andersen thermostat to the system.

Parameters:

targetTemp - Target temperature in Kelvins.

collisionFreq - Collision frequency in 1/psec.

addCOMMRemoverForce

public void addCOMMRemoverForce()

Adds a force that removes center-of-mass motion.

addMonteCarloBarostatForce

public void addMonteCarloBarostatForce(double targetPressure,
 double targetTemp,
 int frequency)

Add a Monte Carlo Barostat to the system.

Parameters:

targetPressure - The target pressure (in atm).

targetTemp - The target temperature.

frequency - The frequency to apply the barostat.

calculateDegreesOfFreedom

public int calculateDegreesOfFreedom()

Calculate the number of degrees of freedom.

Returns:

Number of degrees of freedom.

getTemperature

public double getTemperature(double kineticEnergy)

getForceField

public ForceField getForceField()

Get the ForceField in use.

Returns:

ForceField instance.

getCrystal

public Crystal getCrystal()

Get the Crystal instance.

Returns:

the Crystal instance.

getNumberOfVariables

public int getNumberOfVariables()

Get the number of variables.

Returns:

the number of variables.

free

public void free()

Destroy the system.

setUpdateBondedTerms

public void setUpdateBondedTerms(boolean updateBondedTerms)

updateParameters

public void updateParameters(@Nullable
 Atom[] atoms)

Update parameters if the Use flags and/or Lambda value has changed.

Parameters:

atoms - Atoms in this list are considered.

updateAtomMass

public void updateAtomMass()

This method sets the mass of inactive atoms to zero.

hasAmoebaCavitationForce

public boolean hasAmoebaCavitationForce()