Package ffx.potential

Class ForceFieldEnergyOpenMM.System

java.lang.Object

ffx.potential.ForceFieldEnergyOpenMM.System

Enclosing class:

ForceFieldEnergyOpenMM

public class ForceFieldEnergyOpenMM.System
extends Object

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.

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	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.
void	printLambdaValues()	Print current lambda values.
void	setLambda(double lambda)	Set the overall lambda value for the system.
void	setUpdateBondedTerms(boolean updateBondedTerms)

Methods inherited from class java.lang.Object

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

Method Details

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.

free

public void free()

Destroy the system.

printLambdaValues

public void printLambdaValues()

Print current lambda values.

setLambda

public void setLambda(double lambda)

Set the overall lambda value for the system.

Parameters:

lambda - Current lambda value.

setUpdateBondedTerms

public void setUpdateBondedTerms(boolean updateBondedTerms)