Package ffx.algorithms

Interface AlgorithmFunctions

All Superinterfaces:

PotentialsFunctions

All Known Implementing Classes:

AlgorithmUtils, UIUtils

public interface AlgorithmFunctions
extends PotentialsFunctions

AlgorithmFunctions, on top of the core functionality of PotentialsFunctions, describes additional functionality such as molecular dynamics and L-BFGS local optimization.

This is implemented in two locations: UIUtils in the User Interfaces package, and in AlgorithmsUtils in the Algorithm package.

The UIUtils implementation is the default for Force Field X; on top of the core functionality, it also updates the FFX graphical user interface and tree structure.

The AlgorithmUtils implementation lacks the extra functionality of the UIUtils implementation, and simply accomplishes the required task. This is used by our tests, and is also potentially useful for third parties who would like to use FFX without its GUI.

Author:

Jacob M. Litman, Michael J. Schnieders

Field Summary

Fields inherited from interface ffx.potential.utils.PotentialsFunctions

logger

Method Summary

Modifier and Type	Method	Description
default AlgorithmListener	getDefaultListener()	Returns a default Listener if available (null by default).
void	md(MolecularAssembly assembly, int nStep, double timeStep, double printInterval, double saveInterval, double temperature, boolean initVelocities, File dyn)	Runs molecular dynamics on an assembly.
Potential	minimize(MolecularAssembly assembly, double eps)	Relax the coordinates of a MolecularAssembly and minimize its potential energy

Methods inherited from interface ffx.potential.utils.PotentialsFunctions

close, closeAll, energy, energy, getActiveAssembly, getArguments, getFilter, isLocal, open, open, openAll, openAll, openAll, returnEnergy, save, saveAsPDB, saveAsPDB, saveAsPDB, saveAsPDBinP1, saveAsXYZ, saveAsXYZasReplicates, saveAsXYZinP1, time, versionFile, versionFile

Method Details

getDefaultListener

default AlgorithmListener getDefaultListener()

Returns a default Listener if available (null by default).

Returns:

An AlgorithmListener or null.

md

void md(MolecularAssembly assembly,
 int nStep,
 double timeStep,
 double printInterval,
 double saveInterval,
 double temperature,
 boolean initVelocities,
 File dyn)

Runs molecular dynamics on an assembly.

Parameters:

assembly - a MolecularAssembly object.

nStep - Timesteps

timeStep - Time per step

printInterval - a double.

saveInterval - a double.

temperature - a double.

initVelocities - Initialize velocities from Maxwell-Boltzmann distribution

dyn - Dynamics file

minimize

Potential minimize(MolecularAssembly assembly,
 double eps)

Relax the coordinates of a MolecularAssembly and minimize its potential energy

Parameters:

assembly - a MolecularAssembly object.

eps - RMS gradient convergence criteria

Returns:

A Potential