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) -> AmoebaAngleForce) __init__(self, other) -> AmoebaAngleForce
addAngle((self, particle1, particle2, ...) Add an angle term to the force field.
getAmoebaGlobalAngleCubic((self) -> double) Get the global cubic term
getAmoebaGlobalAnglePentic((self) -> double) Get the global pentic term
getAmoebaGlobalAngleQuartic((self) -> double) Get the global quartic term
getAmoebaGlobalAngleSextic((self) -> double) Get the global sextic term
getAngleParameters(self, index) Get the force field parameters for an angle term.
getForceGroup((self) -> int) Get the force group this Force belongs to.
getNumAngles((self) -> int) 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) -> bool) Returns whether or not this force makes use of periodic boundary conditions.
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
__delattr__

x.__delattr__(‘name’) <==> del x.name

__format__()

default object formatter

__getattribute__

x.__getattribute__(‘name’) <==> x.name

__hash__
__reduce__()

helper for pickle

__reduce_ex__()

helper for pickle

__sizeof__() → int

size of object in memory, in bytes

__str__
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).