AmoebaPiTorsionForce

class simtk.openmm.openmm.AmoebaPiTorsionForce(*args)

This class implements the Amoeba pi-torsion interaction.

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

__init__(self) → AmoebaPiTorsionForce

__init__(self, other) -> AmoebaPiTorsionForce

Create an AmoebaPiTorsionForce.

Methods

__init__((self) -> AmoebaPiTorsionForce) __init__(self, other) -> AmoebaPiTorsionForce
addPiTorsion((self, particle1, particle2, ...) Add a torsion term to the force field.
getForceGroup((self) -> int) Get the force group this Force belongs to.
getNumPiTorsions((self) -> int) Get the number of pi torsion terms in the potential function
getPiTorsionParameters(self, index) Get the force field parameters for a torsion term.
setForceGroup(self, group) Set the force group this Force belongs to.
setPiTorsionParameters(self, index, ...) Set the force field parameters for a pi torsion term.
setUsesPeriodicBoundaryConditions(self, periodic) Set whether this force should apply periodic boundary conditions when calculating displacements.
updateParametersInContext(self, context) Update the per-torsion 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.
getNumPiTorsions(self) → int

Get the number of pi torsion terms in the potential function

addPiTorsion(self, particle1, particle2, particle3, particle4, particle5, particle6, k) → int

Add a torsion term to the force field.

Parameters:
  • particle1 (int) – the index of the first particle connected by the torsion
  • particle2 (int) – the index of the second particle connected by the torsion
  • particle3 (int) – the index of the third particle connected by the torsion
  • particle4 (int) – the index of the fourth particle connected by the torsion
  • particle5 (int) – the index of the fifth particle connected by the torsion
  • particle6 (int) – the index of the sixth particle connected by the torsion
  • k (double) – the force constant for the torsion
Returns:

the index of the torsion that was added

Return type:

int

getPiTorsionParameters(self, index)

Get the force field parameters for a torsion term.

Parameters:index (int) – the index of the torsion for which to get parameters
Returns:
  • particle1 (int) – the index of the first particle connected by the torsion
  • particle2 (int) – the index of the second particle connected by the torsion
  • particle3 (int) – the index of the third particle connected by the torsion
  • particle4 (int) – the index of the fourth particle connected by the torsion
  • particle5 (int) – the index of the fifth particle connected by the torsion
  • particle6 (int) – the index of the sixth particle connected by the torsion
  • k (double) – the force constant for the torsion
setPiTorsionParameters(self, index, particle1, particle2, particle3, particle4, particle5, particle6, k)

Set the force field parameters for a pi torsion term.

Parameters:
  • index (int) – the index of the torsion for which to set parameters
  • particle1 (int) – the index of the first particle connected by the torsion
  • particle2 (int) – the index of the second particle connected by the torsion
  • particle3 (int) – the index of the third particle connected by the torsion
  • particle4 (int) – the index of the fourth particle connected by the torsion
  • particle5 (int) – the index of the fifth particle connected by the torsion
  • particle6 (int) – the index of the sixth particle connected by the torsion
  • k (double) – the force constant for the torsion
updateParametersInContext(self, context)

Update the per-torsion 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 setPiTorsionParameters() 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-torsion parameters. The set of particles involved in a torsion cannot be changed, nor can new torsions 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).