AmoebaStretchBendForce

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

This class implements the Amoeba stretch-bend interaction.

To use it, create a StretchBendForce object then call addStretchBend() once for each stretch-bend. After a stretch-bend has been added, you can modify its force field parameters by calling setStretchBendParameters(). This will have no effect on Contexts that already exist unless you call updateParametersInContext().

__init__(self) → AmoebaStretchBendForce

__init__(self, other) -> AmoebaStretchBendForce

Create an AmoebaStretchBendForce.

Methods

__init__((self) -> AmoebaStretchBendForce) __init__(self, other) -> AmoebaStretchBendForce
addStretchBend((self, particle1, particle2, ...) Add a stretch-bend term to the force field.
getForceGroup((self) -> int) Get the force group this Force belongs to.
getNumStretchBends((self) -> int) Get the number of stretch-bend terms in the potential function
getStretchBendParameters(self, index) Get the force field parameters for a stretch-bend term.
setForceGroup(self, group) Set the force group this Force belongs to.
setStretchBendParameters(self, index, ...) Set the force field parameters for a stretch-bend term.
setUsesPeriodicBoundaryConditions(self, periodic) Set whether this force should apply periodic boundary conditions when calculating displacements.
updateParametersInContext(self, context) Update the per-stretch-bend term 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.
__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).
getNumStretchBends(self) → int

Get the number of stretch-bend terms in the potential function

addStretchBend(self, particle1, particle2, particle3, lengthAB, lengthCB, angle, k1, k2) → int

Add a stretch-bend term to the force field.

Parameters:
  • particle1 (int) – the index of the first particle connected by the stretch-bend
  • particle2 (int) – the index of the second particle connected by the stretch-bend
  • particle3 (int) – the index of the third particle connected by the stretch-bend
  • lengthAB (double) – the equilibrium length of the stretch-bend in bond ab [particle1, particle2], measured in nm
  • lengthCB (double) – the equilibrium length of the stretch-bend in bond cb [particle3, particle2], measured in nm
  • angle (double) – the equilibrium angle in radians
  • k1 (double) – the force constant of the product of bond ab and angle a-b-c
  • k2 (double) – the force constant of the product of bond bc and angle a-b-c (optional, default is the same as k1)
Returns:

the index of the stretch-bend that was added

Return type:

int

getStretchBendParameters(self, index)

Get the force field parameters for a stretch-bend term.

Parameters:index (int) – the index of the stretch-bend for which to get parameters
Returns:
  • particle1 (int) – the index of the first particle connected by the stretch-bend
  • particle2 (int) – the index of the second particle connected by the stretch-bend
  • particle3 (int) – the index of the third particle connected by the stretch-bend
  • lengthAB (double) – the equilibrium length of the stretch-bend in bond ab [particle1, particle2], measured in nm
  • lengthCB (double) – the equilibrium length of the stretch-bend in bond cb [particle3, particle2], measured in nm
  • angle (double) – the equilibrium angle in radians
  • k1 (double) – the force constant of the product of bond ab and angle a-b-c
  • k2 (double) – the force constant of the product of bond bc and angle a-b-c
setStretchBendParameters(self, index, particle1, particle2, particle3, lengthAB, lengthCB, angle, k1, k2)

Set the force field parameters for a stretch-bend term.

Parameters:
  • index (int) – the index of the stretch-bend for which to set parameters
  • particle1 (int) – the index of the first particle connected by the stretch-bend
  • particle2 (int) – the index of the second particle connected by the stretch-bend
  • particle3 (int) – the index of the third particle connected by the stretch-bend
  • lengthAB (double) – the equilibrium length of the stretch-bend in bond ab [particle1, particle2], measured in nm
  • lengthCB (double) – the equilibrium length of the stretch-bend in bond cb [particle3, particle2], measured in nm
  • angle (double) – the equilibrium angle in radians
  • k1 (double) – the force constant of the product of bond ab and angle a-b-c
  • k2 (double) – the force constant of the product of bond bc and angle a-b-c (optional, default is the same as k1)
updateParametersInContext(self, context)

Update the per-stretch-bend term 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 setStretchBendParameters() 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-stretch-bend term parameters. The set of particles involved in a term cannot be changed, nor can new terms 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