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CustomNonbondedForce Class Reference

This class implements nonbonded interactions between particles. More...

+ Inheritance diagram for CustomNonbondedForce:

Public Member Functions

def getNumParticles
 getNumParticles(CustomNonbondedForce self) -> int
 
def getNumExclusions
 getNumExclusions(CustomNonbondedForce self) -> int
 
def getNumPerParticleParameters
 getNumPerParticleParameters(CustomNonbondedForce self) -> int
 
def getNumGlobalParameters
 getNumGlobalParameters(CustomNonbondedForce self) -> int
 
def getNumFunctions
 getNumFunctions(CustomNonbondedForce self) -> int
 
def getEnergyFunction
 getEnergyFunction(CustomNonbondedForce self) -> std::string const &
 
def setEnergyFunction
 setEnergyFunction(CustomNonbondedForce self, std::string const & energy)
 
def getNonbondedMethod
 getNonbondedMethod(CustomNonbondedForce self) -> OpenMM::CustomNonbondedForce::NonbondedMethod
 
def setNonbondedMethod
 setNonbondedMethod(CustomNonbondedForce self, OpenMM::CustomNonbondedForce::NonbondedMethod method)
 
def getCutoffDistance
 getCutoffDistance(CustomNonbondedForce self) -> double
 
def setCutoffDistance
 setCutoffDistance(CustomNonbondedForce self, double distance)
 
def addPerParticleParameter
 addPerParticleParameter(CustomNonbondedForce self, std::string const & name) -> int
 
def getPerParticleParameterName
 getPerParticleParameterName(CustomNonbondedForce self, int index) -> std::string const &
 
def setPerParticleParameterName
 setPerParticleParameterName(CustomNonbondedForce self, int index, std::string const & name)
 
def addGlobalParameter
 addGlobalParameter(CustomNonbondedForce self, std::string const & name, double defaultValue) -> int
 
def getGlobalParameterName
 getGlobalParameterName(CustomNonbondedForce self, int index) -> std::string const &
 
def setGlobalParameterName
 setGlobalParameterName(CustomNonbondedForce self, int index, std::string const & name)
 
def getGlobalParameterDefaultValue
 getGlobalParameterDefaultValue(CustomNonbondedForce self, int index) -> double
 
def setGlobalParameterDefaultValue
 setGlobalParameterDefaultValue(CustomNonbondedForce self, int index, double defaultValue)
 
def addParticle
 addParticle(CustomNonbondedForce self, vectord parameters) -> int
 
def getParticleParameters
 getParticleParameters(CustomNonbondedForce self, int index)
 
def setParticleParameters
 setParticleParameters(CustomNonbondedForce self, int index, vectord parameters)
 
def addExclusion
 addExclusion(CustomNonbondedForce self, int particle1, int particle2) -> int
 
def getExclusionParticles
 getExclusionParticles(CustomNonbondedForce self, int index)
 
def setExclusionParticles
 setExclusionParticles(CustomNonbondedForce self, int index, int particle1, int particle2)
 
def addFunction
 addFunction(CustomNonbondedForce self, std::string const & name, vectord values, double min, double max) -> int
 
def getFunctionParameters
 getFunctionParameters(CustomNonbondedForce self, int index)
 
def setFunctionParameters
 setFunctionParameters(CustomNonbondedForce self, int index, std::string const & name, vectord values, double min, double max)
 
def updateParametersInContext
 updateParametersInContext(CustomNonbondedForce self, Context context)
 
def __init__
 init(OpenMM::CustomNonbondedForce self, std::string const & energy) -> CustomNonbondedForce init(OpenMM::CustomNonbondedForce self, CustomNonbondedForce other) -> CustomNonbondedForce
 
def __del__
 del(OpenMM::CustomNonbondedForce self)
 
- Public Member Functions inherited from Force
def __init__
 
def __del__
 del(OpenMM::Force self)
 
def getForceGroup
 getForceGroup(Force self) -> int
 
def setForceGroup
 setForceGroup(Force self, int group)
 
def __copy__
 
def __deepcopy__
 

Public Attributes

 this
 

Static Public Attributes

 NoCutoff _openmm.CustomNonbondedForce_NoCutoff
 
 CutoffNonPeriodic _openmm.CustomNonbondedForce_CutoffNonPeriodic
 
 CutoffPeriodic _openmm.CustomNonbondedForce_CutoffPeriodic
 

Detailed Description

This class implements nonbonded interactions between particles.

Unlike NonbondedForce, the functional form of the interaction is completely customizable, and may involve arbitrary algebraic expressions and tabulated functions. It may depend on the distance between particles, as well as on arbitrary global and per-particle parameters. It also optionally supports periodic boundary conditions and cutoffs for long range interactions.

To use this class, create a CustomNonbondedForce object, passing an algebraic expression to the constructor that defines the interaction energy between each pair of particles. The expression may depend on r, the distance between the particles, as well as on any parameters you choose. Then call addPerParticleParameter() to define per-particle parameters, and addGlobalParameter() to define global parameters. The values of per-particle parameters are specified as part of the system definition, while values of global parameters may be modified during a simulation by calling Context::setParameter().

Next, call addParticle() once for each particle in the System to set the values of its per-particle parameters. The number of particles for which you set parameters must be exactly equal to the number of particles in the System, or else an exception will be thrown when you try to create a Context. After a particle has been added, you can modify its parameters by calling setParticleParameters(). This will have no effect on Contexts that already exist unless you call updateParametersInContext().

CustomNonbondedForce also lets you specify "exclusions", particular pairs of particles whose interactions should be omitted from force and energy calculations. This is most often used for particles that are bonded to each other.

As an example, the following code creates a CustomNonbondedForce that implements a 12-6 Lennard-Jones potential:

CustomNonbondedForce* force = new CustomNonbondedForce("4*epsilon*((sigma/r)^12-(sigma/r)^6); sigma=0.5*(sigma1+sigma2); epsilon=sqrt(epsilon1*epsilon2)");

This force depends on two parameters: sigma and epsilon. The following code defines these as per-particle parameters:

force->addPerParticleParameter("sigma");
force->addPerParticleParameter("epsilon");

The expression must be symmetric with respect to the two particles. It typically will only be evaluated once for each pair of particles, and no guarantee is made about which particle will be identified as "particle 1". In the above example, the energy only depends on the products sigma1*sigma2 and epsilon1*epsilon2, both of which are unchanged if the labels 1 and 2 are reversed. In contrast, if it depended on the difference sigma1-sigma2, the results would be undefined, because reversing the labels 1 and 2 would change the energy.

Expressions may involve the operators + (add), - (subtract), * (multiply), / (divide), and ^ (power), and the following functions: sqrt, exp, log, sin, cos, sec, csc, tan, cot, asin, acos, atan, sinh, cosh, tanh, erf, erfc, min, max, abs, step, delta. All trigonometric functions are defined in radians, and log is the natural logarithm. step(x) = 0 if x is less than 0, 1 otherwise. delta(x) = 1 if x is 0, 0 otherwise. The names of per-particle parameters have the suffix "1" or "2" appended to them to indicate the values for the two interacting particles. As seen in the above example, the expression may also involve intermediate quantities that are defined following the main expression, using ";" as a separator.

In addition, you can call addFunction() to define a new function based on tabulated values. You specify a vector of values, and a natural spline is created from them. That function can then appear in the expression.

Constructor & Destructor Documentation

def __init__ (   self,
  args 
)

init(OpenMM::CustomNonbondedForce self, std::string const & energy) -> CustomNonbondedForce init(OpenMM::CustomNonbondedForce self, CustomNonbondedForce other) -> CustomNonbondedForce

Create a CustomNonbondedForce.

Parameters
energyan algebraic expression giving the interaction energy between two particles as a function of r, the distance between them, as well as any global and per-particle parameters
def __del__ (   self)

del(OpenMM::CustomNonbondedForce self)

Member Function Documentation

def addExclusion (   self,
  args 
)

addExclusion(CustomNonbondedForce self, int particle1, int particle2) -> int

Add a particle pair to the list of interactions that should be excluded.

Parameters
particle1the index of the first particle in the pair
particle2the index of the second particle in the pair
def addFunction (   self,
  args 
)

addFunction(CustomNonbondedForce self, std::string const & name, vectord values, double min, double max) -> int

Add a tabulated function that may appear in the energy expression.

Parameters
namethe name of the function as it appears in expressions
valuesthe tabulated values of the function f(x) at uniformly spaced values of x between min and max. The function is assumed to be zero for x < min or x > max.
minthe value of the independent variable corresponding to the first element of values
maxthe value of the independent variable corresponding to the last element of values
def addGlobalParameter (   self,
  args 
)

addGlobalParameter(CustomNonbondedForce self, std::string const & name, double defaultValue) -> int

Add a new global parameter that the interaction may depend on.

Parameters
namethe name of the parameter
defaultValuethe default value of the parameter
def addParticle (   self,
  args 
)

addParticle(CustomNonbondedForce self, vectord parameters) -> int

Add the nonbonded force parameters for a particle. This should be called once for each particle in the System. When it is called for the i'th time, it specifies the parameters for the i'th particle.

Parameters
parametersthe list of parameters for the new particle
def addPerParticleParameter (   self,
  args 
)

addPerParticleParameter(CustomNonbondedForce self, std::string const & name) -> int

Add a new per-particle parameter that the interaction may depend on.

Parameters
namethe name of the parameter
def getCutoffDistance (   self)

getCutoffDistance(CustomNonbondedForce self) -> double

Get the cutoff distance (in nm) being used for nonbonded interactions. If the NonbondedMethod in use is NoCutoff, this value will have no effect.

def getEnergyFunction (   self)

getEnergyFunction(CustomNonbondedForce self) -> std::string const &

Get the algebraic expression that gives the interaction energy between two particles

def getExclusionParticles (   self,
  args 
)

getExclusionParticles(CustomNonbondedForce self, int index)

Get the particles in a pair whose interaction should be excluded.

Parameters
indexthe index of the exclusion for which to get particle indices
particle1the index of the first particle in the pair
particle2the index of the second particle in the pair
def getFunctionParameters (   self,
  args 
)

getFunctionParameters(CustomNonbondedForce self, int index)

Get the parameters for a tabulated function that may appear in the energy expression.

Parameters
indexthe index of the function for which to get parameters
namethe name of the function as it appears in expressions
valuesthe tabulated values of the function f(x) at uniformly spaced values of x between min and max. The function is assumed to be zero for x < min or x > max.
minthe value of the independent variable corresponding to the first element of values
maxthe value of the independent variable corresponding to the last element of values
def getGlobalParameterDefaultValue (   self,
  args 
)

getGlobalParameterDefaultValue(CustomNonbondedForce self, int index) -> double

Get the default value of a global parameter.

Parameters
indexthe index of the parameter for which to get the default value
def getGlobalParameterName (   self,
  args 
)

getGlobalParameterName(CustomNonbondedForce self, int index) -> std::string const &

Get the name of a global parameter.

Parameters
indexthe index of the parameter for which to get the name
def getNonbondedMethod (   self)

getNonbondedMethod(CustomNonbondedForce self) -> OpenMM::CustomNonbondedForce::NonbondedMethod

Get the method used for handling long range nonbonded interactions.

def getNumExclusions (   self)

getNumExclusions(CustomNonbondedForce self) -> int

Get the number of particle pairs whose interactions should be excluded.

def getNumFunctions (   self)

getNumFunctions(CustomNonbondedForce self) -> int

Get the number of tabulated functions that have been defined.

def getNumGlobalParameters (   self)

getNumGlobalParameters(CustomNonbondedForce self) -> int

Get the number of global parameters that the interaction depends on.

def getNumParticles (   self)

getNumParticles(CustomNonbondedForce self) -> int

Get the number of particles for which force field parameters have been defined.

def getNumPerParticleParameters (   self)

getNumPerParticleParameters(CustomNonbondedForce self) -> int

Get the number of per-particle parameters that the interaction depends on.

def getParticleParameters (   self,
  args 
)

getParticleParameters(CustomNonbondedForce self, int index)

Get the nonbonded force parameters for a particle.

Parameters
indexthe index of the particle for which to get parameters
parametersthe list of parameters for the specified particle
def getPerParticleParameterName (   self,
  args 
)

getPerParticleParameterName(CustomNonbondedForce self, int index) -> std::string const &

Get the name of a per-particle parameter.

Parameters
indexthe index of the parameter for which to get the name
def setCutoffDistance (   self,
  args 
)

setCutoffDistance(CustomNonbondedForce self, double distance)

Set the cutoff distance (in nm) being used for nonbonded interactions. If the NonbondedMethod in use is NoCutoff, this value will have no effect.

Parameters
distancethe cutoff distance, measured in nm
def setEnergyFunction (   self,
  args 
)

setEnergyFunction(CustomNonbondedForce self, std::string const & energy)

Set the algebraic expression that gives the interaction energy between two particles

def setExclusionParticles (   self,
  args 
)

setExclusionParticles(CustomNonbondedForce self, int index, int particle1, int particle2)

Set the particles in a pair whose interaction should be excluded.

Parameters
indexthe index of the exclusion for which to set particle indices
particle1the index of the first particle in the pair
particle2the index of the second particle in the pair
def setFunctionParameters (   self,
  args 
)

setFunctionParameters(CustomNonbondedForce self, int index, std::string const & name, vectord values, double min, double max)

Set the parameters for a tabulated function that may appear in algebraic expressions.

Parameters
indexthe index of the function for which to set parameters
namethe name of the function as it appears in expressions
valuesthe tabulated values of the function f(x) at uniformly spaced values of x between min and max. The function is assumed to be zero for x < min or x > max.
minthe value of the independent variable corresponding to the first element of values
maxthe value of the independent variable corresponding to the last element of values
def setGlobalParameterDefaultValue (   self,
  args 
)

setGlobalParameterDefaultValue(CustomNonbondedForce self, int index, double defaultValue)

Set the default value of a global parameter.

Parameters
indexthe index of the parameter for which to set the default value
namethe default value of the parameter
def setGlobalParameterName (   self,
  args 
)

setGlobalParameterName(CustomNonbondedForce self, int index, std::string const & name)

Set the name of a global parameter.

Parameters
indexthe index of the parameter for which to set the name
namethe name of the parameter
def setNonbondedMethod (   self,
  args 
)

setNonbondedMethod(CustomNonbondedForce self, OpenMM::CustomNonbondedForce::NonbondedMethod method)

Set the method used for handling long range nonbonded interactions.

def setParticleParameters (   self,
  args 
)

setParticleParameters(CustomNonbondedForce self, int index, vectord parameters)

Set the nonbonded force parameters for a particle.

Parameters
indexthe index of the particle for which to set parameters
parametersthe list of parameters for the specified particle
def setPerParticleParameterName (   self,
  args 
)

setPerParticleParameterName(CustomNonbondedForce self, int index, std::string const & name)

Set the name of a per-particle parameter.

Parameters
indexthe index of the parameter for which to set the name
namethe name of the parameter
def updateParametersInContext (   self,
  args 
)

updateParametersInContext(CustomNonbondedForce self, Context context)

Update the per-particle 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 setParticleParameters() to modify this object's parameters, then call updateParametersInState() to copy them over to the Context.

This method has several limitations. The only information it updates is the values of per-particle parameters. All other aspects of the Force (the energy function, nonbonded method, cutoff distance, etc.) are unaffected and can only be changed by reinitializing the Context. Also, this method cannot be used to add new particles, only to change the parameters of existing ones.

Member Data Documentation

CutoffNonPeriodic _openmm.CustomNonbondedForce_CutoffNonPeriodic
static
CutoffPeriodic _openmm.CustomNonbondedForce_CutoffPeriodic
static
NoCutoff _openmm.CustomNonbondedForce_NoCutoff
static
this

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