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AmoebaStretchBendForce Class Reference

This class implements the Amoeba stretch-bend interaction. More...

+ Inheritance diagram for AmoebaStretchBendForce:

Public Member Functions

def getNumStretchBends
 getNumStretchBends(AmoebaStretchBendForce self) -> int More...
 
def addStretchBend
 addStretchBend(AmoebaStretchBendForce self, int particle1, int particle2, int particle3, double lengthAB, double lengthCB, double angle, double k) -> int More...
 
def getStretchBendParameters
 getStretchBendParameters(AmoebaStretchBendForce self, int index) More...
 
def setStretchBendParameters
 setStretchBendParameters(AmoebaStretchBendForce self, int index, int particle1, int particle2, int particle3, double lengthAB, double lengthCB, double angle, double k) More...
 
def updateParametersInContext
 updateParametersInContext(AmoebaStretchBendForce self, Context context) More...
 
def __init__
 init(OpenMM::AmoebaStretchBendForce self) -> AmoebaStretchBendForce init(OpenMM::AmoebaStretchBendForce self, AmoebaStretchBendForce other) -> AmoebaStretchBendForce More...
 
def __del__
 del(OpenMM::AmoebaStretchBendForce self) More...
 
- Public Member Functions inherited from Force
def __init__
 
def __del__
 del(OpenMM::Force self) More...
 
def getForceGroup
 getForceGroup(Force self) -> int More...
 
def setForceGroup
 setForceGroup(Force self, int group) More...
 
def __copy__
 
def __deepcopy__
 

Public Attributes

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Detailed Description

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().

Constructor & Destructor Documentation

def __init__ (   self,
  args 
)

init(OpenMM::AmoebaStretchBendForce self) -> AmoebaStretchBendForce init(OpenMM::AmoebaStretchBendForce self, AmoebaStretchBendForce other) -> AmoebaStretchBendForce

Create an AmoebaStretchBendForce.

References simtk.openmm.openmm.stripUnits().

def __del__ (   self)

del(OpenMM::AmoebaStretchBendForce self)

References simtk.openmm.openmm.stripUnits().

Member Function Documentation

def addStretchBend (   self,
  args 
)

addStretchBend(AmoebaStretchBendForce self, int particle1, int particle2, int particle3, double lengthAB, double lengthCB, double angle, double k) -> int

Add a stretch-bend term to the force field.

Parameters
particle1the index of the first particle connected by the stretch-bend
particle2the index of the second particle connected by the stretch-bend
particle3the index of the third particle connected by the stretch-bend
lengthABthe equilibrium length of the stretch-bend in bond ab [particle1, particle2], measured in nm
lengthCBthe equilibrium length of the stretch-bend in bond cb [particle3, particle2], measured in nm
anglethe equilibrium angle in radians
kthe force constant for the stretch-bend

References simtk.openmm.openmm.stripUnits().

def getNumStretchBends (   self)

getNumStretchBends(AmoebaStretchBendForce self) -> int

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

References simtk.openmm.openmm.stripUnits().

def getStretchBendParameters (   self,
  args 
)

getStretchBendParameters(AmoebaStretchBendForce self, int index)

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

Parameters
indexthe index of the stretch-bend for which to get parameters
particle1the index of the first particle connected by the stretch-bend
particle2the index of the second particle connected by the stretch-bend
particle3the index of the third particle connected by the stretch-bend
lengthABthe equilibrium length of the stretch-bend in bond ab [particle1, particle2], measured in nm
lengthCBthe equilibrium length of the stretch-bend in bond cb [particle3, particle2], measured in nm
anglethe equilibrium angle in radians
kthe force constant for the stretch-bend

References simtk.openmm.openmm.stripUnits().

def setStretchBendParameters (   self,
  args 
)

setStretchBendParameters(AmoebaStretchBendForce self, int index, int particle1, int particle2, int particle3, double lengthAB, double lengthCB, double angle, double k)

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

Parameters
indexthe index of the stretch-bend for which to set parameters
particle1the index of the first particle connected by the stretch-bend
particle2the index of the second particle connected by the stretch-bend
particle3the index of the third particle connected by the stretch-bend
lengthABthe equilibrium length of the stretch-bend in bond ab [particle1, particle2], measured in nm
lengthCBthe equilibrium length of the stretch-bend in bond cb [particle3, particle2], measured in nm
anglethe equilibrium angle in radians
kthe force constant for the stretch-bend

References simtk.openmm.openmm.stripUnits().

def updateParametersInContext (   self,
  args 
)

updateParametersInContext(AmoebaStretchBendForce self, Context 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 updateParametersInState() 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.

References simtk.openmm.openmm.stripUnits().

Member Data Documentation

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The documentation for this class was generated from the following file: