AmoebaAngleForce¶

class simtk.openmm.openmm.AmoebaAngleForce(*args)¶

This class implements an interaction between triplets of particles that varies with the angle between them. The interaction is defined by a 6th order polynomial. Only the quadratic term is set per-angle. The coefficients of the higher order terms each have a single value that is set globally.

To use it, create an AmoebaAngleForce object then call addAngle() once for each angle. After an angle has been added, you can modify its force field parameters by calling setAngleParameters(). This will have no effect on Contexts that already exist unless you call updateParametersInContext().

__init__(self) → AmoebaAngleForce¶: __init__(self, other) -> AmoebaAngleForce Create an AmoebaAngleForce.

Methods

`__init__`(self)	__init__(self, other) -> AmoebaAngleForce Create an AmoebaAngleForce.
`addAngle`(self, particle1, particle2, …)	Add an angle term to the force field.
`getAmoebaGlobalAngleCubic`(self)	Get the global cubic term
`getAmoebaGlobalAnglePentic`(self)	Get the global pentic term
`getAmoebaGlobalAngleQuartic`(self)	Get the global quartic term
`getAmoebaGlobalAngleSextic`(self)	Get the global sextic term
`getAngleParameters`(self, index)	Get the force field parameters for an angle term.
`getForceGroup`(self)	Get the force group this Force belongs to.
`getNumAngles`(self)	Get the number of angle stretch terms in the potential function
`setAmoebaGlobalAngleCubic`(self, cubicK)	Set the global cubic term
`setAmoebaGlobalAnglePentic`(self, penticK)	Set the global pentic term
`setAmoebaGlobalAngleQuartic`(self, quarticK)	Set the global quartic term
`setAmoebaGlobalAngleSextic`(self, sexticK)	Set the global sextic term
`setAngleParameters`(self, index, particle1, …)	Set the force field parameters for an angle term.
`setForceGroup`(self, group)	Set the force group this Force belongs to.
`setUsesPeriodicBoundaryConditions`(self, periodic)	Set whether this force should apply periodic boundary conditions when calculating displacements.
`updateParametersInContext`(self, context)	Update the per-angle parameters in a Context to match those stored in this Force object.
`usesPeriodicBoundaryConditions`(self)	Returns whether or not this force makes use of periodic boundary conditions.

Attributes

thisown

The membership flag

property thisown¶: The membership flag

getNumAngles(self) → int¶: Get the number of angle stretch terms in the potential function

setAmoebaGlobalAngleCubic(self, cubicK)¶

Set the global cubic term

Parameters: cubicK (double) – the cubic force constant for the angle

getAmoebaGlobalAngleCubic(self) → double¶

Get the global cubic term

Returns: global cubicK term
Return type: double

setAmoebaGlobalAngleQuartic(self, quarticK)¶

Set the global quartic term

Parameters: quarticK (double) – the quartic force constant for the angle

getAmoebaGlobalAngleQuartic(self) → double¶

Get the global quartic term

Returns: global quartic term
Return type: double

setAmoebaGlobalAnglePentic(self, penticK)¶

Set the global pentic term

Parameters: penticK (double) – the pentic force constant for the angle

getAmoebaGlobalAnglePentic(self) → double¶

Get the global pentic term

Returns: global penticK term
Return type: double

setAmoebaGlobalAngleSextic(self, sexticK)¶

Set the global sextic term

Parameters: sexticK (double) – the sextic force constant for the angle

getAmoebaGlobalAngleSextic(self) → double¶

Get the global sextic term

Returns: global sextic term
Return type: double

addAngle(self, particle1, particle2, particle3, length, quadraticK) → int¶

Add an angle term to the force field.

Parameters

particle1 (int) – the index of the first particle connected by the angle
particle2 (int) – the index of the second particle connected by the angle
particle3 (int) – the index of the third particle connected by the angle
length (double) – the equilibrium angle, measured in degrees
quadraticK (double) – the quadratic force constant for the angle, measured in kJ/mol/radian^2

Returns

the index of the angle that was added

Return type

int

getAngleParameters(self, index)¶

Get the force field parameters for an angle term.

Parameters

index (int) – the index of the angle for which to get parameters

Returns

particle1 (int) – the index of the first particle connected by the angle
particle2 (int) – the index of the second particle connected by the angle
particle3 (int) – the index of the third particle connected by the angle
length (double) – the equilibrium angle, measured in degrees
quadraticK (double) – the quadratic force constant for the angle, measured in kJ/mol/radian^2

setAngleParameters(self, index, particle1, particle2, particle3, length, quadraticK)¶

Set the force field parameters for an angle term.

Parameters

index (int) – the index of the angle for which to set parameters
particle1 (int) – the index of the first particle connected by the angle
particle2 (int) – the index of the second particle connected by the angle
particle3 (int) – the index of the third particle connected by the angle
length (double) – the equilibrium angle, measured in degrees
quadraticK (double) – the quadratic force constant for the angle, measured in kJ/mol/radian^2

updateParametersInContext(self, context)¶

Update the per-angle parameters in a Context to match those stored in this Force object. This method provides an efficient method to update certain parameters in an existing Context without needing to reinitialize it. Simply call setAngleParameters() to modify this object’s parameters, then call updateParametersInContext() to copy them over to the Context.

The only information this method updates is the values of per-angle parameters. The set of particles involved in an angle cannot be changed, nor can new angles be added.

setUsesPeriodicBoundaryConditions(self, periodic)¶: Set whether this force should apply periodic boundary conditions when calculating displacements. Usually this is not appropriate for bonded forces, but there are situations when it can be useful.

usesPeriodicBoundaryConditions(self) → bool¶

Returns whether or not this force makes use of periodic boundary conditions.

Returns: true if force uses PBC and false otherwise
Return type: bool

__copy__(self) → Force¶

getForceGroup(self) → int¶: Get the force group this Force belongs to.

setForceGroup(self, group)¶

Set the force group this Force belongs to.

Parameters: group (int) – the group index. Legal values are between 0 and 31 (inclusive).