Package ffx.openmm

Class LangevinMiddleIntegrator

java.lang.Object

ffx.openmm.Integrator

ffx.openmm.LangevinMiddleIntegrator

Direct Known Subclasses:

LangevinIntegrator

public class LangevinMiddleIntegrator
extends Integrator

This is an Integrator which simulates a System using Langevin dynamics, with the LFMiddle discretization (J. Phys. Chem. A 2019, 123, 28, 6056-6079). This method tend to produce more accurate configurational sampling than other discretizations, such as the one used in LangevinIntegrator.

The algorithm is closely related to the BAOAB discretization (Proc. R. Soc. A. 472: 20160138). Both methods produce identical trajectories, but LFMiddle returns half step (leapfrog) velocities, while BAOAB returns on-step velocities. The former provide a much more accurate sampling of the thermal ensemble.

Field Summary

Fields inherited from class ffx.openmm.Integrator

pointer

Constructor Summary

Constructors

Constructor	Description
LangevinMiddleIntegrator(double dt, double temp, double gamma)	Create a LangevinMiddleIntegrator.

Method Summary

Modifier and Type	Method	Description
void	destroy()	Destroy the integrator.
double	getFriction()	Get the friction coefficient.
int	getRandomNumberSeed()	Get the random number seed.
double	getTemperature()	Get the temperature.
void	setFriction(double gamma)	Set the friction coefficient.
void	setRandomNumberSeed(int seed)	Set the random number seed.
void	setTemperature(double temp)	Set the temperature.
void	step(int steps)	Step the integrator.

Methods inherited from class ffx.openmm.Integrator

getConstraintTolerance, getIntegrationForceGroups, getPointer, getStepSize, setConstraintTolerance, setIntegrationForceGroups, setPointer, setStepSize

Methods inherited from class java.lang.Object

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

Constructor Details

LangevinMiddleIntegrator

public LangevinMiddleIntegrator(double dt,
 double temp,
 double gamma)

Create a LangevinMiddleIntegrator.

Parameters:

dt - the step size with which to integrate the system (in picoseconds)

temp - the temperature of the heat bath (in Kelvin)

gamma - the friction coefficient which couples the system to the heat bath (in inverse picoseconds)

Method Details

destroy

public void destroy()

Destroy the integrator.

Specified by:

destroy in class Integrator

getFriction

public double getFriction()

Get the friction coefficient.

Returns:

The friction coefficient in inverse picoseconds.

getRandomNumberSeed

public int getRandomNumberSeed()

Get the random number seed.

Returns:

The random number seed.

getTemperature

public double getTemperature()

Get the temperature.

Returns:

The temperature in Kelvin.

setFriction

public void setFriction(double gamma)

Set the friction coefficient.

Parameters:

gamma - The friction coefficient in inverse picoseconds.

setRandomNumberSeed

public void setRandomNumberSeed(int seed)

Set the random number seed.

Parameters:

seed - The random number seed.

setTemperature

public void setTemperature(double temp)

Set the temperature.

Parameters:

temp - The temperature in Kelvin.

step

public void step(int steps)

Step the integrator.

Overrides:

step in class Integrator

Parameters:

steps - The number of steps to take.