RBTorsionForce

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

This class implements an interaction between groups of four particles that varies with the torsion angle between them according to the Ryckaert-Bellemans potential. To use it, create an RBTorsionForce object then call addTorsion() once for each torsion. After a torsion has been added, you can modify its force field parameters by calling setTorsionParameters(). This will have no effect on Contexts that already exist unless you call updateParametersInContext().

__init__(self) → RBTorsionForce

__init__(self, other) -> RBTorsionForce

Create a RBTorsionForce.

Methods

__init__((self) -> RBTorsionForce) __init__(self, other) -> RBTorsionForce
addTorsion((self, particle1, particle2, ...) Add a Ryckaert-Bellemans torsion term to the force field.
getForceGroup((self) -> int) Get the force group this Force belongs to.
getNumTorsions((self) -> int) Get the number of Ryckaert-Bellemans torsion terms in the potential function
getTorsionParameters(self, index) Get the force field parameters for a Ryckaert-Bellemans torsion term.
setForceGroup(self, group) Set the force group this Force belongs to.
setTorsionParameters(self, index, particle1, ...) Set the force field parameters for a Ryckaert-Bellemans 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.
getNumTorsions(self) → int

Get the number of Ryckaert-Bellemans torsion terms in the potential function

addTorsion(self, particle1, particle2, particle3, particle4, c0, c1, c2, c3, c4, c5) → int

Add a Ryckaert-Bellemans torsion term to the force field.

Parameters:
  • particle1 (int) – the index of the first particle forming the torsion
  • particle2 (int) – the index of the second particle forming the torsion
  • particle3 (int) – the index of the third particle forming the torsion
  • particle4 (int) – the index of the fourth particle forming the torsion
  • c0 (double) – the coefficient of the constant term, measured in kJ/mol
  • c1 (double) – the coefficient of the 1st order term, measured in kJ/mol
  • c2 (double) – the coefficient of the 2nd order term, measured in kJ/mol
  • c3 (double) – the coefficient of the 3rd order term, measured in kJ/mol
  • c4 (double) – the coefficient of the 4th order term, measured in kJ/mol
  • c5 (double) – the coefficient of the 5th order term, measured in kJ/mol
Returns:

the index of the torsion that was added

Return type:

int

getTorsionParameters(self, index)

Get the force field parameters for a Ryckaert-Bellemans torsion term.

Parameters:index (int) – the index of the torsion for which to get parameters
Returns:
  • particle1 (int) – the index of the first particle forming the torsion
  • particle2 (int) – the index of the second particle forming the torsion
  • particle3 (int) – the index of the third particle forming the torsion
  • particle4 (int) – the index of the fourth particle forming the torsion
  • c0 (double) – the coefficient of the constant term, measured in kJ/mol
  • c1 (double) – the coefficient of the 1st order term, measured in kJ/mol
  • c2 (double) – the coefficient of the 2nd order term, measured in kJ/mol
  • c3 (double) – the coefficient of the 3rd order term, measured in kJ/mol
  • c4 (double) – the coefficient of the 4th order term, measured in kJ/mol
  • c5 (double) – the coefficient of the 5th order term, measured in kJ/mol
setTorsionParameters(self, index, particle1, particle2, particle3, particle4, c0, c1, c2, c3, c4, c5)

Set the force field parameters for a Ryckaert-Bellemans torsion term.

Parameters:
  • index (int) – the index of the torsion for which to set parameters
  • particle1 (int) – the index of the first particle forming the torsion
  • particle2 (int) – the index of the second particle forming the torsion
  • particle3 (int) – the index of the third particle forming the torsion
  • particle4 (int) – the index of the fourth particle forming the torsion
  • c0 (double) – the coefficient of the constant term, measured in kJ/mol
  • c1 (double) – the coefficient of the 1st order term, measured in kJ/mol
  • c2 (double) – the coefficient of the 2nd order term, measured in kJ/mol
  • c3 (double) – the coefficient of the 3rd order term, measured in kJ/mol
  • c4 (double) – the coefficient of the 4th order term, measured in kJ/mol
  • c5 (double) – the coefficient of the 5th order term, measured in kJ/mol
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 setTorsionParameters() 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).