Package ffx.potential.nonbonded.implicit

Class GaussVol

java.lang.Object

ffx.potential.nonbonded.implicit.GaussVol

public class GaussVol
extends Object

GaussVol implements a description molecular volume and surface area described by overlapping Gaussian spheres.

Ported from C++ code by Emilio Gallicchio. GaussVol is part of the AGBNP/OpenMM implicit solvent model.

Since:

1.0

Author:

Michael J. Schnieders

See Also:

• Zhang, B., Kilburg, D., Eastman, P., Pande, V. S., and Gallicchio, E. (2017). Efficient gaussian density formulation of volume and surface areas of macromolecules on graphical processing units. Journal of Computational Chemistry, 38(10), 740-752.

Field Summary

Fields

Modifier and Type	Field	Description
static final double	DEFAULT_GAUSSVOL_RADII_OFFSET	Default offset applied to radii for use with Gaussian Volumes to correct for not including hydrogen atoms.
static final double	DEFAULT_GAUSSVOL_RADII_SCALE	Default scaling applied to radii for use with Gaussian Volumes to correct for not including hydrogen atoms and general underestimation of molecular volume

Constructor Summary

Constructors

Constructor	Description
GaussVol(Atom[] atoms, ForceField forceField, ParallelTeam parallelTeam)	Creates/Initializes a GaussVol instance.

Method Summary

Modifier and Type	Method	Description
void	allocate(Atom[] atoms)
double	computeVolumeAndSA(double[][] positions)	Compute molecular volume and surface area.
int	getMaximumDepth()	Returns the maximum depth of the overlap tree
double[]	getRadii()	Get the radii.
double[]	getSelfVolumeFractions()	Return the self volume fraction for each atom.
double	getSurfaceArea()	Return Surface Area (A^2).
double[]	getSurfaceAreaGradient()
int	getTotalNumberOfOverlaps()	Return the total number of overlaps in the tree
double	getVolume()	Return Volume (A^3).
double[]	getVolumeGradient()
void	updateAtom(int i)

Methods inherited from class java.lang.Object

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

Field Details

DEFAULT_GAUSSVOL_RADII_OFFSET

public static final double DEFAULT_GAUSSVOL_RADII_OFFSET

Default offset applied to radii for use with Gaussian Volumes to correct for not including hydrogen atoms.

See Also:

• Constant Field Values

DEFAULT_GAUSSVOL_RADII_SCALE

public static final double DEFAULT_GAUSSVOL_RADII_SCALE

Default scaling applied to radii for use with Gaussian Volumes to correct for not including hydrogen atoms and general underestimation of molecular volume

Default set to 1.15 to match Corrigan et al. 2023 protein model Can be set to greater than 1.0 to increase the radii by a uniform percentage (ex: a radii scale of 1.25 increases all radii by 25%)

See Also:

• Constant Field Values

Constructor Details

GaussVol

public GaussVol(Atom[] atoms,
 ForceField forceField,
 ParallelTeam parallelTeam)

Creates/Initializes a GaussVol instance.

Parameters:

atoms - The atoms to examine.

forceField - The ForceField in use.

parallelTeam - ParallelTeam for Parallal jobs.

Method Details

getRadii

public double[] getRadii()

Get the radii.

Returns:

Returns the radii.

getSelfVolumeFractions

public double[] getSelfVolumeFractions()

Return the self volume fraction for each atom.

Returns:

The self-volume fractions.

computeVolumeAndSA

public double computeVolumeAndSA(double[][] positions)

Compute molecular volume and surface area.

Parameters:

positions - Atomic positions to use.

Returns:

The volume.

getMaximumDepth

public int getMaximumDepth()

Returns the maximum depth of the overlap tree

Returns:

maximumDepth

getSurfaceArea

public double getSurfaceArea()

Return Surface Area (A^2).

Returns:

Surface Area (A^2).

getSurfaceAreaGradient

public double[] getSurfaceAreaGradient()

getTotalNumberOfOverlaps

public int getTotalNumberOfOverlaps()

Return the total number of overlaps in the tree

Returns:

totalNumberOfOverlaps

getVolume

public double getVolume()

Return Volume (A^3).

Returns:

Volume (A^3).

getVolumeGradient

public double[] getVolumeGradient()

allocate

public void allocate(Atom[] atoms)
              throws Exception

Throws:

Exception

updateAtom

public void updateAtom(int i)