CustomGBForce Class Reference

This class implements complex, multiple stage nonbonded interactions between particles. More...

Inheritance diagram for CustomGBForce:
Force

List of all members.

Public Member Functions

def getNumParticles
 getNumParticles(self) -> int
def getNumExclusions
 getNumExclusions(self) -> int
def getNumPerParticleParameters
 getNumPerParticleParameters(self) -> int
def getNumGlobalParameters
 getNumGlobalParameters(self) -> int
def getNumFunctions
 getNumFunctions(self) -> int
def getNumComputedValues
 getNumComputedValues(self) -> int
def getNumEnergyTerms
 getNumEnergyTerms(self) -> int
def getNonbondedMethod
 getNonbondedMethod(self) -> NonbondedMethod
def setNonbondedMethod
 setNonbondedMethod(self, NonbondedMethod method)
def getCutoffDistance
 getCutoffDistance(self) -> double
def setCutoffDistance
 setCutoffDistance(self, double distance)
def addPerParticleParameter
 addPerParticleParameter(self, string name) -> int
def getPerParticleParameterName
 getPerParticleParameterName(self, int index) -> string
def setPerParticleParameterName
 setPerParticleParameterName(self, int index, string name)
def addGlobalParameter
 addGlobalParameter(self, string name, double defaultValue) -> int
def getGlobalParameterName
 getGlobalParameterName(self, int index) -> string
def setGlobalParameterName
 setGlobalParameterName(self, int index, string name)
def getGlobalParameterDefaultValue
 getGlobalParameterDefaultValue(self, int index) -> double
def setGlobalParameterDefaultValue
 setGlobalParameterDefaultValue(self, int index, double defaultValue)
def addParticle
 addParticle(self, vectord parameters) -> int
def getParticleParameters
 getParticleParameters(self, int index)
def setParticleParameters
 setParticleParameters(self, int index, vectord parameters)
def addComputedValue
 addComputedValue(self, string name, string expression, ComputationType type) -> int
def getComputedValueParameters
 getComputedValueParameters(self, int index)
def setComputedValueParameters
 setComputedValueParameters(self, int index, string name, string expression, ComputationType type)
def addEnergyTerm
 addEnergyTerm(self, string expression, ComputationType type) -> int
def getEnergyTermParameters
 getEnergyTermParameters(self, int index)
def setEnergyTermParameters
 setEnergyTermParameters(self, int index, string expression, ComputationType type)
def addExclusion
 addExclusion(self, int particle1, int particle2) -> int
def getExclusionParticles
 getExclusionParticles(self, int index)
def setExclusionParticles
 setExclusionParticles(self, int index, int particle1, int particle2)
def addFunction
 addFunction(self, string name, vectord values, double min, double max) -> int
def getFunctionParameters
 getFunctionParameters(self, int index)
def setFunctionParameters
 setFunctionParameters(self, int index, string name, vectord values, double min, double max)
def __init__
 __init__(self) -> CustomGBForce __init__(self, CustomGBForce other) -> CustomGBForce
def __del__
 __del__(self)

Public Attributes

 this

Static Public Attributes

 NoCutoff = _openmm.CustomGBForce_NoCutoff
 CutoffNonPeriodic = _openmm.CustomGBForce_CutoffNonPeriodic
 CutoffPeriodic = _openmm.CustomGBForce_CutoffPeriodic
 SingleParticle = _openmm.CustomGBForce_SingleParticle
 ParticlePair = _openmm.CustomGBForce_ParticlePair
 ParticlePairNoExclusions = _openmm.CustomGBForce_ParticlePairNoExclusions

Detailed Description

This class implements complex, multiple stage nonbonded interactions between particles.

It is designed primarily for implementing Generalized Born implicit solvation models, although it is not strictly limited to that purpose. The interaction is specified as a series of computations, each defined by an arbitrary algebraic expression. It also allows tabulated functions to be defined and used with the computations. It optionally supports periodic boundary conditions and cutoffs for long range interactions.

The computation consists of calculating some number of per-particle computed values, followed by one or more energy terms. A computed value is a scalar value that is computed for each particle in the system. It may depend on an arbitrary set of global and per-particle parameters, and well as on other computed values that have been calculated before it. Once all computed values have been calculated, the energy terms and their derivatives are evaluated to determine the system energy and particle forces. The energy terms may depend on global parameters, per-particle parameters, and per-particle computed values.

When specifying a computed value or energy term, you provide an algebraic expression to evaluate and a computation type describing how the expression is to be evaluated. There are two main types of computations:

Be aware that, although this class is extremely general in the computations it can define, particular Platforms may only support more restricted types of computations. In particular, all currently existing Platforms require that the first computed value must be a particle pair computation, and all computed values after the first must be single particle computations. This is sufficient for most Generalized Born models, but might not permit some other types of calculations to be implemented.

This is a complicated class to use, and an example may help to clarify it. The following code implements the OBC variant of the GB/SA solvation model, using the ACE approximation to estimate surface area:

     CustomGBForce* custom = new CustomGBForce();
     custom->addPerParticleParameter("q");
     custom->addPerParticleParameter("radius");
     custom->addPerParticleParameter("scale");
     custom->addGlobalParameter("solventDielectric", obc->getSolventDielectric());
     custom->addGlobalParameter("soluteDielectric", obc->getSoluteDielectric());
     custom->addComputedValue("I", "step(r+sr2-or1)*0.5*(1/L-1/U+0.25*(1/U^2-1/L^2)*(r-sr2*sr2/r)+0.5*log(L/U)/r+C);"
                                   "U=r+sr2;"
                                   "C=2*(1/or1-1/L)*step(sr2-r-or1);"
                                   "L=max(or1, D);"
                                   "D=abs(r-sr2);"
                                   "sr2 = scale2*or2;"
                                   "or1 = radius1-0.009; or2 = radius2-0.009", CustomGBForce.ParticlePairNoExclusions);
     custom->addComputedValue("B", "1/(1/or-tanh(1*psi-0.8*psi^2+4.85*psi^3)/radius);"
                                   "psi=I*or; or=radius-0.009", CustomGBForce.SingleParticle);
     custom->addEnergyTerm("28.3919551*(radius+0.14)^2*(radius/B)^6-0.5*138.935456*(1/soluteDielectric-1/solventDielectric)*q^2/B",
                           CustomGBForce.SingleParticle);
     custom->addEnergyTerm("-138.935456*(1/soluteDielectric-1/solventDielectric)*q1*q2/f;"
                           "f=sqrt(r^2+B1*B2*exp(-r^2/(4*B1*B2)))", CustomGBForce.ParticlePair);

It begins by defining three per-particle parameters (charge, atomic radius, and scale factor) and two global parameters (the dielectric constants for the solute and solvent). It then defines a computed value "I" of type ParticlePair. The expression for evaluating it is a complicated function of the distance between each pair of particles (r), their atomic radii (radius1 and radius2), and their scale factors (scale1 and scale2). Very roughly speaking, it is a measure of the distance between each particle and other nearby particles.

Next a computation is defined for the Born Radius (B). It is computed independently for each particle, and is a function of that particle's atomic radius and the intermediate value I defined above.

Finally, two energy terms are defined. The first one is computed for each particle and represents the surface area term, as well as the self interaction part of the polarization energy. The second term is calculated for each pair of particles, and represents the screening of electrostatic interactions by the solvent.

After defining the force as shown above, you should then call addParticle() once for each particle in the System to set the values of its per-particle parameters (q, radius, and scale). 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().

CustomNonbondedForce also lets you specify "exclusions", particular pairs of particles whose interactions should be omitted from calculations. This is most often used for particles that are bonded to each other. Even if you specify exclusions, however, you can use the computation type ParticlePairNoExclusions to indicate that exclusions should not be applied to a particular piece of the computation.

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. All trigonometric functions are defined in radians, and log is the natural logarithm. step(x) = 0 if x is less than 0, 1 otherwise. In expressions for particle pair calculations, the names of per-particle parameters and computed values have the suffix "1" or "2" appended to them to indicate the values for the two interacting particles. As seen in the above example, an 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 expressions.

Member Function Documentation

def __del__ (   self  ) 

__del__(self)

Reimplemented from Force.

def __init__ (   self,
  args 
)

__init__(self) -> CustomGBForce __init__(self, CustomGBForce other) -> CustomGBForce

Create a CustomGBForce.

def addComputedValue (   self,
  args 
)

addComputedValue(self, string name, string expression, ComputationType type) -> int

Add a computed value to calculate for each particle.

Parameters:
name the name of the value
expression an algebraic expression to evaluate when calculating the computed value. If the ComputationType is SingleParticle, the expression is evaluated independently for each particle, and may depend on its x, y, and z coordinates, as well as the per-particle parameters and previous computed values for that particle. If the ComputationType is ParticlePair or ParticlePairNoExclusions, the expression is evaluated once for every other particle in the system and summed to get the final value. In the latter case, the expression may depend on the distance r between the two particles, and on the per-particle parameters and previous computed values for each of them. Append "1" to a variable name to indicate the parameter for the particle whose value is being calculated, and "2" to indicate the particle it is interacting with.
type the method to use for computing this value
def addEnergyTerm (   self,
  args 
)

addEnergyTerm(self, string expression, ComputationType type) -> int

Add a term to the energy computation.

Parameters:
expression an algebraic expression to evaluate when calculating the energy. If the ComputationType is SingleParticle, the expression is evaluated once for each particle, and may depend on its x, y, and z coordinates, as well as the per-particle parameters and computed values for that particle. If the ComputationType is ParticlePair or ParticlePairNoExclusions, the expression is evaluated once for every pair of particles in the system. In the latter case, the expression may depend on the distance r between the two particles, and on the per-particle parameters and computed values for each of them. Append "1" to a variable name to indicate the parameter for the first particle in the pair and "2" to indicate the second particle in the pair.
type the method to use for computing this value
def addExclusion (   self,
  args 
)

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

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

Parameters:
particle1 the index of the first particle in the pair
particle2 the index of the second particle in the pair
def addFunction (   self,
  args 
)

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

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

Parameters:
name the name of the function as it appears in expressions
values the 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.
min the value of the independent variable corresponding to the first element of values
max the value of the independent variable corresponding to the last element of values
def addGlobalParameter (   self,
  args 
)

addGlobalParameter(self, string name, double defaultValue) -> int

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

Parameters:
name the name of the parameter
defaultValue the default value of the parameter
def addParticle (   self,
  args 
)

addParticle(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:
parameters the list of parameters for the new particle
def addPerParticleParameter (   self,
  args 
)

addPerParticleParameter(self, string name) -> int

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

Parameters:
name the name of the parameter
def getComputedValueParameters (   self,
  args 
)

getComputedValueParameters(self, int index)

Get the properties of a computed value.

Parameters:
index the index of the computed value for which to get parameters
name the name of the value
expression an algebraic expression to evaluate when calculating the computed value. If the ComputationType is SingleParticle, the expression is evaluated independently for each particle, and may depend on its x, y, and z coordinates, as well as the per-particle parameters and previous computed values for that particle. If the ComputationType is ParticlePair or ParticlePairNoExclusions, the expression is evaluated once for every other particle in the system and summed to get the final value. In the latter case, the expression may depend on the distance r between the two particles, and on the per-particle parameters and previous computed values for each of them. Append "1" to a variable name to indicate the parameter for the particle whose value is being calculated, and "2" to indicate the particle it is interacting with.
type the method to use for computing this value
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.

def getEnergyTermParameters (   self,
  args 
)

getEnergyTermParameters(self, int index)

Get the properties of a term to the energy computation.

Parameters:
index the index of the term for which to get parameters
expression an algebraic expression to evaluate when calculating the energy. If the ComputationType is SingleParticle, the expression is evaluated once for each particle, and may depend on its x, y, and z coordinates, as well as the per-particle parameters and computed values for that particle. If the ComputationType is ParticlePair or ParticlePairNoExclusions, the expression is evaluated once for every pair of particles in the system. In the latter case, the expression may depend on the distance r between the two particles, and on the per-particle parameters and computed values for each of them. Append "1" to a variable name to indicate the parameter for the first particle in the pair and "2" to indicate the second particle in the pair.
type the method to use for computing this value
def getExclusionParticles (   self,
  args 
)

getExclusionParticles(self, int index)

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

Parameters:
index the index of the exclusion for which to get particle indices
particle1 the index of the first particle in the pair
particle2 the index of the second particle in the pair
def getFunctionParameters (   self,
  args 
)

getFunctionParameters(self, int index)

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

Parameters:
index the index of the function for which to get parameters
name the name of the function as it appears in expressions
values the 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.
min the value of the independent variable corresponding to the first element of values
max the value of the independent variable corresponding to the last element of values
def getGlobalParameterDefaultValue (   self,
  args 
)

getGlobalParameterDefaultValue(self, int index) -> double

Get the default value of a global parameter.

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

getGlobalParameterName(self, int index) -> string

Get the name of a global parameter.

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

getNonbondedMethod(self) -> NonbondedMethod

Get the method used for handling long range nonbonded interactions.

def getNumComputedValues (   self  ) 

getNumComputedValues(self) -> int

Get the number of per-particle computed values the interaction depends on.

def getNumEnergyTerms (   self  ) 

getNumEnergyTerms(self) -> int

Get the number of terms in the energy computation.

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 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 getParticleParameters (   self,
  args 
)

getParticleParameters(self, int index)

Get the nonbonded force parameters for a particle.

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

getPerParticleParameterName(self, int index) -> string

Get the name of a per-particle parameter.

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

setComputedValueParameters(self, int index, string name, string expression, ComputationType type)

Set the properties of a computed value.

Parameters:
index the index of the computed value for which to set parameters
name the name of the value
expression an algebraic expression to evaluate when calculating the computed value. If the ComputationType is SingleParticle, the expression is evaluated independently for each particle, and may depend on its x, y, and z coordinates, as well as the per-particle parameters and previous computed values for that particle. If the ComputationType is ParticlePair or ParticlePairNoExclusions, the expression is evaluated once for every other particle in the system and summed to get the final value. In the latter case, the expression may depend on the distance r between the two particles, and on the per-particle parameters and previous computed values for each of them. Append "1" to a variable name to indicate the parameter for the particle whose value is being calculated, and "2" to indicate the particle it is interacting with.
type the method to use for computing this value
def setCutoffDistance (   self,
  args 
)

setCutoffDistance(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:
distance the cutoff distance, measured in nm
def setEnergyTermParameters (   self,
  args 
)

setEnergyTermParameters(self, int index, string expression, ComputationType type)

Set the properties of a term to the energy computation.

Parameters:
index the index of the term for which to set parameters
expression an algebraic expression to evaluate when calculating the energy. If the ComputationType is SingleParticle, the expression is evaluated once for each particle, and may depend on its x, y, and z coordinates, as well as the per-particle parameters and computed values for that particle. If the ComputationType is ParticlePair or ParticlePairNoExclusions, the expression is evaluated once for every pair of particles in the system. In the latter case, the expression may depend on the distance r between the two particles, and on the per-particle parameters and computed values for each of them. Append "1" to a variable name to indicate the parameter for the first particle in the pair and "2" to indicate the second particle in the pair.
type the method to use for computing this value
def setExclusionParticles (   self,
  args 
)

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

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

Parameters:
index the index of the exclusion for which to set particle indices
particle1 the index of the first particle in the pair
particle2 the index of the second particle in the pair
def setFunctionParameters (   self,
  args 
)

setFunctionParameters(self, int index, string name, vectord values, double min, double max)

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

Parameters:
index the index of the function for which to set parameters
name the name of the function as it appears in expressions
values the 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.
min the value of the independent variable corresponding to the first element of values
max the value of the independent variable corresponding to the last element of values
def setGlobalParameterDefaultValue (   self,
  args 
)

setGlobalParameterDefaultValue(self, int index, double defaultValue)

Set the default value of a global parameter.

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

setGlobalParameterName(self, int index, string name)

Set the name of a global parameter.

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

setNonbondedMethod(self, NonbondedMethod method)

Set the method used for handling long range nonbonded interactions.

def setParticleParameters (   self,
  args 
)

setParticleParameters(self, int index, vectord parameters)

Set the nonbonded force parameters for a particle.

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

setPerParticleParameterName(self, int index, string name)

Set the name of a per-particle parameter.

Parameters:
index the index of the parameter for which to set the name
name the name of the parameter

Member Data Documentation

CutoffNonPeriodic = _openmm.CustomGBForce_CutoffNonPeriodic [static]
CutoffPeriodic = _openmm.CustomGBForce_CutoffPeriodic [static]
NoCutoff = _openmm.CustomGBForce_NoCutoff [static]
ParticlePair = _openmm.CustomGBForce_ParticlePair [static]
ParticlePairNoExclusions = _openmm.CustomGBForce_ParticlePairNoExclusions [static]
SingleParticle = _openmm.CustomGBForce_SingleParticle [static]
this
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