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

Inheritance diagram for CustomNonbondedForce:

Public Member Functions
def	__init__
	__init__(self, energy) -> CustomNonbondedForce __init__(self, rhs) -> CustomNonbondedForce
def	getNumParticles
	getNumParticles(self) -> int
def	getNumExclusions
	getNumExclusions(self) -> int
def	getNumPerParticleParameters
	getNumPerParticleParameters(self) -> int
def	getNumGlobalParameters
	getNumGlobalParameters(self) -> int
def	getNumTabulatedFunctions
	getNumTabulatedFunctions(self) -> int
def	getNumFunctions
	getNumFunctions(self) -> int
def	getNumInteractionGroups
	getNumInteractionGroups(self) -> int
def	getEnergyFunction
	getEnergyFunction(self) -> std::string const &
def	setEnergyFunction
	Set the algebraic expression that gives the interaction energy between two particles.
def	getNonbondedMethod
	getNonbondedMethod(self) -> OpenMM::CustomNonbondedForce::NonbondedMethod
def	setNonbondedMethod
	Set the method used for handling long range nonbonded interactions.
def	getCutoffDistance
	getCutoffDistance(self) -> double
def	setCutoffDistance
	Set the cutoff distance (in nm) being used for nonbonded interactions.
def	getUseSwitchingFunction
	getUseSwitchingFunction(self) -> bool
def	setUseSwitchingFunction
	Set whether a switching function is applied to the interaction.
def	getSwitchingDistance
	getSwitchingDistance(self) -> double
def	setSwitchingDistance
	Set the distance at which the switching function begins to reduce the interaction.
def	getUseLongRangeCorrection
	getUseLongRangeCorrection(self) -> bool
def	setUseLongRangeCorrection
	Set whether to add a correction to the energy to compensate for the cutoff and switching function.
def	addPerParticleParameter
	addPerParticleParameter(self, name) -> int
def	getPerParticleParameterName
	getPerParticleParameterName(self, index) -> std::string const &
def	setPerParticleParameterName
	Set the name of a per-particle parameter.
def	addGlobalParameter
	addGlobalParameter(self, name, defaultValue) -> int
def	getGlobalParameterName
	getGlobalParameterName(self, index) -> std::string const &
def	setGlobalParameterName
	Set the name of a global parameter.
def	getGlobalParameterDefaultValue
	getGlobalParameterDefaultValue(self, index) -> double
def	setGlobalParameterDefaultValue
	Set the default value of a global parameter.
def	addParticle
	addParticle(self, parameters) -> int addParticle(self) -> int
def	getParticleParameters
	Get the nonbonded force parameters for a particle.
def	setParticleParameters
	Set the nonbonded force parameters for a particle.
def	addExclusion
	addExclusion(self, particle1, particle2) -> int
def	getExclusionParticles
	Get the particles in a pair whose interaction should be excluded.
def	setExclusionParticles
	Set the particles in a pair whose interaction should be excluded.
def	createExclusionsFromBonds
	Identify exclusions based on the molecular topology.
def	addTabulatedFunction
	addTabulatedFunction(self, name, function) -> int
def	getTabulatedFunction
	getTabulatedFunction(self, index) -> TabulatedFunction getTabulatedFunction(self, index) -> TabulatedFunction
def	getTabulatedFunctionName
	getTabulatedFunctionName(self, index) -> std::string const &
def	addFunction
	addFunction(self, name, values, min, max) -> int
def	getFunctionParameters
	Get the parameters for a tabulated function that may appear in the energy expression.
def	setFunctionParameters
	Set the parameters for a tabulated function that may appear in the energy expression.
def	addInteractionGroup
	addInteractionGroup(self, set1, set2) -> int
def	getInteractionGroupParameters
	Get the parameters for an interaction group.
def	setInteractionGroupParameters
	Set the parameters for an interaction group.
def	updateParametersInContext
	Update the per-particle parameters in a Context to match those stored in this Force object.
def	usesPeriodicBoundaryConditions
	usesPeriodicBoundaryConditions(self) -> bool
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.

CustomNonbondedForce can operate in two modes. By default, it computes the interaction of every particle in the System with every other particle. Alternatively, you can restrict it to only a subset of particle pairs. To do this, specify one or more "interaction groups". An interaction group consists of two sets of particles that should interact with each other. Every particle in the first set interacts with every particle in the second set. For example, you might use this feature to compute a solute-solvent interaction energy, while omitting all interactions between two solute atoms or two solvent atoms.

To create an interaction group, call addInteractionGroup(). You may add as many interaction groups as you want. Be aware of the following:

Exclusions are still taken into account, so the interactions between excluded pairs are omitted.
Likewise, a particle will never interact with itself, even if it appears in both sets of an interaction group.
If a particle pair appears in two different interaction groups, its interaction will be computed twice. This is sometimes useful, but be aware of it so you do not accidentally create unwanted duplicate interactions.
If you do not add any interaction groups to a CustomNonbondedForce, it operates in the default mode where every particle interacts with every other particle.

When using a cutoff, by default the interaction is sharply truncated at the cutoff distance. Optionally you can instead use a switching function to make the interaction smoothly go to zero over a finite distance range. To enable this, call setUseSwitchingFunction(). You must also call setSwitchingDistance() to specify the distance at which the interaction should begin to decrease. The switching distance must be less than the cutoff distance. Of course, you could also incorporate the switching function directly into your energy expression, but there are several advantages to keeping it separate. It makes your energy expression simpler to write and understand. It allows you to use the same energy expression with or without a cutoff. Also, when using a long range correction (see below), separating out the switching function allows the correction to be calculated more accurately.

Another optional feature of this class is to add a contribution to the energy which approximates the effect of all interactions beyond the cutoff in a periodic system. When running a simulation at constant pressure, this can improve the quality of the result. Call setUseLongRangeCorrection() to enable it.

Computing the long range correction takes negligible work in each time step, but it does require an expensive precomputation at the start of the simulation. Furthermore, that precomputation must be repeated every time a global parameter changes (or when you modify per-particle parameters by calling updateParametersInContext()). This means that if parameters change frequently, the long range correction can be very slow. For this reason, it is disabled by default.

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, floor, ceil, step, delta, select. 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. select(x,y,z) = z if x = 0, y 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 addTabulatedFunction() to define a new function based on tabulated values. You specify the function by creating a TabulatedFunction object. That function can then appear in the expression.

Constructor & Destructor Documentation

def __init__	(	self,
		args
	)

__init__(self, energy) -> CustomNonbondedForce __init__(self, rhs) -> CustomNonbondedForce

Create a CustomNonbondedForce.

Parameters:

energy (string) an 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

Member Function Documentation

def addExclusion	(	self,
		particle1,
		particle2
	)

addExclusion(self, particle1, particle2) -> int

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

In many cases, you can use createExclusionsFromBonds() rather than adding each exclusion explicitly.

Parameters:

particle1	(int) the index of the first particle in the pair
particle2	(int) the index of the second particle in the pair

Returns:: (int) the index of the exclusion that was added

def addFunction	(	self,
		name,
		values,
		min,
		max
	)

addFunction(self, name, values, min, max) -> int

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

def addGlobalParameter	(	self,
		name,
		defaultValue
	)

addGlobalParameter(self, name, defaultValue) -> int

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

Parameters:

name	(string) the name of the parameter
defaultValue	(double) the default value of the parameter

Returns:: (int) the index of the parameter that was added

def addInteractionGroup	(	self,
		set1,
		set2
	)

addInteractionGroup(self, set1, set2) -> int

Add an interaction group. An interaction will be computed between every particle in set1 and every particle in set2.

Parameters:

set1	(set< int >) the first set of particles forming the interaction group
set2	(set< int >) the second set of particles forming the interaction group

Returns:: (int) the index of the interaction group that was added

def addParticle	(	self,
		args
	)

addParticle(self, parameters) -> int addParticle(self) -> 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:

parameters (vector< double >) the list of parameters for the new particle

Returns:: (int) the index of the particle that was added

def addPerParticleParameter	(	self,
		name
	)

addPerParticleParameter(self, name) -> int

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

Parameters:

name	(string) the name of the parameter

Returns:: (int) the index of the parameter that was added

def addTabulatedFunction	(	self,
		name,
		function
	)

addTabulatedFunction(self, name, function) -> int

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

Parameters:

name	(string) the name of the function as it appears in expressions
function	(TabulatedFunction *) a TabulatedFunction object defining the function. The TabulatedFunction should have been created on the heap with the "new" operator. The Force takes over ownership of it, and deletes it when the Force itself is deleted.

Returns:: (int) the index of the function that was added

def createExclusionsFromBonds	(	self,
		bonds,
		bondCutoff
	)

Identify exclusions based on the molecular topology.

Particles which are separated by up to a specified number of bonds are added as exclusions.

Parameters:

bonds	(vector< std::pair< int, int > >) the set of bonds based on which to construct exclusions. Each element specifies the indices of two particles that are bonded to each other.
bondCutoff	(int) pairs of particles that are separated by this many bonds or fewer are added to the list of exclusions

def getCutoffDistance ( self )

getCutoffDistance(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.

Returns:: (double) the cutoff distance, measured in nm

def getEnergyFunction ( self )

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

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

def getExclusionParticles	(	self,
		index
	)

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

Parameters:

index (int) the index of the exclusion for which to get particle indices

Returns:: (int) the index of the first particle in the pair; (int) the index of the second particle in the pair

def getFunctionParameters	(	self,
		index
	)

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

def getGlobalParameterDefaultValue	(	self,
		index
	)

getGlobalParameterDefaultValue(self, index) -> double

Get the default value of a global parameter.

Parameters:

index (int) the index of the parameter for which to get the default value

Returns:: (double) the parameter default value

def getGlobalParameterName	(	self,
		index
	)

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

Get the name of a global parameter.

Parameters:

index (int) the index of the parameter for which to get the name

Returns:: (string) the parameter name

def getInteractionGroupParameters	(	self,
		index
	)

Get the parameters for an interaction group.

Parameters:

index (int) the index of the interaction group for which to get parameters

Returns:: (set< int >) the first set of particles forming the interaction group; (set< int >) the second set of particles forming the interaction group

def getNonbondedMethod ( self )

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

Get the method used for handling long range nonbonded interactions.

def getNumExclusions ( self )

getNumExclusions(self) -> int

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

def getNumFunctions ( self )

getNumFunctions(self) -> int

Get the number of tabulated functions that have been defined.

def getNumGlobalParameters ( self )

getNumGlobalParameters(self) -> int

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

def getNumInteractionGroups ( self )

getNumInteractionGroups(self) -> int

Get the number of interaction groups that have been defined.

def getNumParticles ( self )

getNumParticles(self) -> int

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

def getNumPerParticleParameters ( self )

getNumPerParticleParameters(self) -> int

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

def getNumTabulatedFunctions ( self )

getNumTabulatedFunctions(self) -> int

Get the number of tabulated functions that have been defined.

def getParticleParameters	(	self,
		index
	)

Get the nonbonded force parameters for a particle.

Parameters:

index (int) the index of the particle for which to get parameters

Returns:: (vector< double >) the list of parameters for the specified particle

def getPerParticleParameterName	(	self,
		index
	)

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

Get the name of a per-particle parameter.

Parameters:

index (int) the index of the parameter for which to get the name

Returns:: (string) the parameter name

def getSwitchingDistance ( self )

getSwitchingDistance(self) -> double

Get the distance at which the switching function begins to reduce the interaction. This must be less than the cutoff distance.

def getTabulatedFunction	(	self,
		args
	)

getTabulatedFunction(self, index) -> TabulatedFunction getTabulatedFunction(self, index) -> TabulatedFunction

Get a reference to a tabulated function that may appear in the energy expression.

Parameters:

index (int) the index of the function to get

Returns:: (TabulatedFunction) the TabulatedFunction object defining the function

def getTabulatedFunctionName	(	self,
		index
	)

getTabulatedFunctionName(self, index) -> std::string const &

Get the name of a tabulated function that may appear in the energy expression.

Parameters:

index (int) the index of the function to get

Returns:: (string) the name of the function as it appears in expressions

def getUseLongRangeCorrection ( self )

getUseLongRangeCorrection(self) -> bool

Get whether to add a correction to the energy to compensate for the cutoff and switching function. This has no effect if periodic boundary conditions are not used.

def getUseSwitchingFunction ( self )

getUseSwitchingFunction(self) -> bool

Get whether a switching function is applied to the interaction. If the nonbonded method is set to NoCutoff, this option is ignored.

def setCutoffDistance	(	self,
		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:

distance (double) the cutoff distance, measured in nm

def setEnergyFunction	(	self,
		energy
	)

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

def setExclusionParticles	(	self,
		index,
		particle1,
		particle2
	)

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

Parameters:

index	(int) the index of the exclusion for which to set particle indices
particle1	(int) the index of the first particle in the pair
particle2	(int) the index of the second particle in the pair

def setFunctionParameters	(	self,
		index,
		name,
		values,
		min,
		max
	)

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

def setGlobalParameterDefaultValue	(	self,
		index,
		defaultValue
	)

Set the default value of a global parameter.

Parameters:

index	(int) the index of the parameter for which to set the default value
defaultValue	(double) the default value of the parameter

def setGlobalParameterName	(	self,
		index,
		name
	)

Set the name of a global parameter.

Parameters:

index	(int) the index of the parameter for which to set the name
name	(string) the name of the parameter

def setInteractionGroupParameters	(	self,
		index,
		set1,
		set2
	)

Set the parameters for an interaction group.

Parameters:

index	(int) the index of the interaction group for which to set parameters
set1	(set< int >) the first set of particles forming the interaction group
set2	(set< int >) the second set of particles forming the interaction group

def setNonbondedMethod	(	self,
		method
	)

Set the method used for handling long range nonbonded interactions.

def setParticleParameters	(	self,
		index,
		parameters
	)

Set the nonbonded force parameters for a particle.

Parameters:

index	(int) the index of the particle for which to set parameters
parameters	(vector< double >) the list of parameters for the specified particle

def setPerParticleParameterName	(	self,
		index,
		name
	)

Set the name of a per-particle parameter.

Parameters:

index	(int) the index of the parameter for which to set the name
name	(string) the name of the parameter

def setSwitchingDistance	(	self,
		distance
	)

Set the distance at which the switching function begins to reduce the interaction.

This must be less than the cutoff distance.

def setUseLongRangeCorrection	(	self,
		use
	)

Set whether to add a correction to the energy to compensate for the cutoff and switching function.

This has no effect if periodic boundary conditions are not used.

def setUseSwitchingFunction	(	self,
		use
	)

Set whether a switching function is applied to the interaction.

If the nonbonded method is set to NoCutoff, this option is ignored.

def updateParametersInContext	(	self,
		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 updateParametersInContext() 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.

def usesPeriodicBoundaryConditions ( self )

usesPeriodicBoundaryConditions(self) -> bool

Returns whether or not this force makes use of periodic boundary conditions.

Returns:: (bool) true if force uses PBC and false otherwise

Reimplemented from Force.

Member Data Documentation

CutoffNonPeriodic = _openmm.CustomNonbondedForce_CutoffNonPeriodic [static]

CutoffPeriodic = _openmm.CustomNonbondedForce_CutoffPeriodic [static]

NoCutoff = _openmm.CustomNonbondedForce_NoCutoff [static]

this

Reimplemented from Force.

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

openmm.py

Public Member Functions

Public Attributes

Static Public Attributes

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation