Package ffx.potential.constraint

Class ShakeChargeConstraint

java.lang.Object

ffx.potential.constraint.ShakeChargeConstraint

All Implemented Interfaces:

Constraint

public class ShakeChargeConstraint
extends Object
implements Constraint

Constructor Summary

Constructors

Constructor	Description
ShakeChargeConstraint(int nConstraints, int c, double tol)

Method Summary

Modifier and Type	Method	Description
void	applyChargeConstraintToStep(double[] x, double[] afric, double[] masses, double dt)	This method follows the SHAKE Charge Constraint laid out in Appendix B of Donnini, Serena, et al.
void	applyConstraintToStep(double[] xPrior, double[] xNew, double[] masses, double tol)	Applies this Constraint in the context of a partially calculated MD time-step.
void	applyConstraintToVelocities(double[] x, double[] v, double[] masses, double tol)	Applies this Constraint to velocities, ensuring relative velocities are perpendicular to constrained bonds, etc., without affecting positions.
int[]	constrainedAtomIndices()	Returns the atomic XYZ indices of all Atoms constrained.
boolean	constraintSatisfied(double[] x, double tol)	Checks if this Constraint is satisfied.
boolean	constraintSatisfied(double[] x, double[] v, double xTol, double vTol)	Checks if this Constraint is satisfied.
int	getNumDegreesFrozen()	Returns the number of degrees of freedom this Constraint constrains.

Methods inherited from class java.lang.Object

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

Constructor Details

ShakeChargeConstraint

public ShakeChargeConstraint(int nConstraints,
 int c,
 double tol)

Method Details

applyConstraintToStep

public void applyConstraintToStep(double[] xPrior,
 double[] xNew,
 double[] masses,
 double tol)

Description copied from interface: Constraint

Applies this Constraint in the context of a partially calculated MD time-step. All arrays are globally indexed (i.e. includes all system atoms, not just the constrained ones).

If there is no prior step (e.g. a newly loaded system that has not yet been rigidified), xPrior and xNew can be copies of each other when passed to the method.

xPrior corresponds to atomCoordinates in the OpenMM constraint code. Ours will be in Angstroms, not nm. xNew corresponds to atomCoordinatesP in the OpenMM constraint code. Ours will be in Angstroms, not nm.

Specified by:

applyConstraintToStep in interface Constraint

Parameters:

xPrior - Atomic coordinates prior to the time-step to be constrained.

xNew - Atomic coordinates after the time-step; updated in-place to satisfy the constraint.

masses - Masses.

tol - Acceptable constraint tolerance for numerical methods, as a fraction of bond length.

applyChargeConstraintToStep

public void applyChargeConstraintToStep(double[] x,
 double[] afric,
 double[] masses,
 double dt)

This method follows the SHAKE Charge Constraint laid out in Appendix B of Donnini, Serena, et al. "Charge-neutral constant pH molecular dynamics simulations using a parsimonious proton buffer." Journal of chemical theory and computation 12.3 (2016): 1040-1051. https://pubs.acs.org/doi/epdf/10.1021/acs.jctc.5b01160

Parameters:

x -

afric -

masses -

dt -

applyConstraintToVelocities

public void applyConstraintToVelocities(double[] x,
 double[] v,
 double[] masses,
 double tol)

Description copied from interface: Constraint

Applies this Constraint to velocities, ensuring relative velocities are perpendicular to constrained bonds, etc., without affecting positions. All arrays are globally indexed (i.e. includes all system atoms, not just the constrained ones).

Our positions will be in Angstroms, and velocities in Angstroms/ps, compared to the OpenMM nm and nm/ps.

Specified by:

applyConstraintToVelocities in interface Constraint

Parameters:

x - Atomic coordinates (unchanged).

v - Velocities (updated in-place to satisfy constraints).

masses - Masses.

tol - Acceptable constraint tolerance for numerical methods; likely in Angstroms/ps

constrainedAtomIndices

public int[] constrainedAtomIndices()

Description copied from interface: Constraint

Returns the atomic XYZ indices of all Atoms constrained. Guaranteed to be unique. The primary assumption will be that variables are in sets of 3x Cartesian coordinates.

Specified by:

constrainedAtomIndices in interface Constraint

Returns:

All indices of constrained Atoms.

constraintSatisfied

public boolean constraintSatisfied(double[] x,
 double tol)

Description copied from interface: Constraint

Checks if this Constraint is satisfied.

Specified by:

constraintSatisfied in interface Constraint

Parameters:

x - Input coordinates to check.

tol - Numerical tolerance as a fraction of bond stretch.

Returns:

Whether this Constraint is satisfied.

constraintSatisfied

public boolean constraintSatisfied(double[] x,
 double[] v,
 double xTol,
 double vTol)

Description copied from interface: Constraint

Checks if this Constraint is satisfied. Also checks velocities; bond constraints, for example, require that relative velocity be orthogonal to the bond. If the velocities vector is null or the tolerance is zero, velocity checks are skipped.

Specified by:

constraintSatisfied in interface Constraint

Parameters:

x - Input coordinates to check.

v - Input velocities to check. If null, velocity check disabled.

xTol - Numerical tolerance for bond lengths.

vTol - Numerical tolerance for velocity checks (typically in degrees). If zero, velocity check disabled.

Returns:

Whether this Constraint is satisfied.

getNumDegreesFrozen

public int getNumDegreesFrozen()

Description copied from interface: Constraint

Returns the number of degrees of freedom this Constraint constrains.

Specified by:

getNumDegreesFrozen in interface Constraint

Returns:

Number of frozen DoF.