Package ffx.algorithms.dynamics.integrators

Class Respa

java.lang.Object

ffx.algorithms.dynamics.integrators.Integrator

ffx.algorithms.dynamics.integrators.Respa

public class Respa
extends Integrator

Respa performs multiple time step molecular dynamics using the reversible reference system propagation algorithm (r-RESPA) via a Verlet core with the potential split into fast- and slow-evolving portions.

The inner RESPA loop is position Verlet.

D. D. Humphreys, R. A. Friesner and B. J. Berne, "A Multiple-Time-Step Molecular Dynamics Algorithm for Macromolecules", Journal of Physical Chemistry, 98, 6885-6892 (1994)

X. Qian and T. Schlick, "Efficient Multiple-Time-Step Integrators with Distance-Based Force Splitting for Particle-Mesh-Ewald Molecular Dynamics Simulations", Journal of Chemical Physics, 115, 4019-4029 (2001)

Since:

1.0

Author:

Gaurav Chattree

Field Summary

Fields inherited from class ffx.algorithms.dynamics.integrators.Integrator

constraints, constraintTolerance, dt, state, useConstraints

Constructor Summary

Constructors

Constructor	Description
Respa(SystemState state)	Initialize Respa multiple time step molecular dynamics.

Method Summary

Modifier and Type	Method	Description
double	getHalfStepEnergy()	Get the potential energy of the fast degrees of freedom.
void	postForce(double[] gradient)	Integrator post-force evaluation operation.
void	preForce(Potential potential)	Integrator pre-force evaluation operation.
void	setInnerTimeSteps(int n)	Set inner Respa number of time steps.
void	setTimeStep(double dt)	Set the time step.
String	toString()

Methods inherited from class ffx.algorithms.dynamics.integrators.Integrator

addConstraints, copyAccelerationToPrevious, getConstraints, getTimeStep, parseIntegrator

Methods inherited from class java.lang.Object

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

Constructor Details

Respa

public Respa(SystemState state)

Initialize Respa multiple time step molecular dynamics.

Parameters:

state - The molecular dynamics state to be operated on.

Method Details

getHalfStepEnergy

public double getHalfStepEnergy()

Get the potential energy of the fast degrees of freedom.

Returns:

The potential energy of the fast degrees of freedom.

postForce

public void postForce(double[] gradient)

Integrator post-force evaluation operation.

The Respa full-step integration operation.

Specified by:

postForce in class Integrator

Parameters:

gradient - the gradient for the post-force operation.

preForce

public void preForce(Potential potential)

Integrator pre-force evaluation operation.

Performs the inner RESPA loop via position Verlet.

Specified by:

preForce in class Integrator

Parameters:

potential - the Potential this integrator operates on.

setInnerTimeSteps

public void setInnerTimeSteps(int n)

Set inner Respa number of time steps.

Parameters:

n - Number of inner time steps (must be greater than or equal to 2).

setTimeStep

public void setTimeStep(double dt)

Set the time step.

Set outer Respa time step.

Specified by:

setTimeStep in class Integrator

Parameters:

dt - the time step (psec).

toString

public String toString()

Overrides:

toString in class Object