OpenMM

This class implements complex, multiple stage nonbonded interactions between particles. More...
Public Member Functions  
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  getNumComputedValues 
getNumComputedValues(self) > int  
def  getNumEnergyTerms 
getNumEnergyTerms(self) > int  
def  getNonbondedMethod 
getNonbondedMethod(self) > OpenMM::CustomGBForce::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  addPerParticleParameter 
addPerParticleParameter(self, name) > int  
def  getPerParticleParameterName 
getPerParticleParameterName(self, index) > std::string const &  
def  setPerParticleParameterName 
Set the name of a perparticle 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  addComputedValue 
addComputedValue(self, name, expression, type) > int  
def  getComputedValueParameters 
Get the properties of a computed value.  
def  setComputedValueParameters 
Set the properties of a computed value.  
def  addEnergyTerm 
addEnergyTerm(self, expression, type) > int  
def  getEnergyTermParameters 
Get the properties of a term to the energy computation.  
def  setEnergyTermParameters 
Set the properties of a term to the energy computation.  
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  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 expressions.  
def  setFunctionParameters 
Set the parameters for a tabulated function that may appear in expressions.  
def  updateParametersInContext 
Update the perparticle parameters in a Context to match those stored in this Force object.  
def  usesPeriodicBoundaryConditions 
usesPeriodicBoundaryConditions(self) > bool  
def  __init__ 
__init__(self) > CustomGBForce __init__(self, other) > CustomGBForce  
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 
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 perparticle _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 perparticle 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, perparticle parameters, and perparticle 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+sr2or1)*0.5*(1/L1/U+0.25*(1/U^21/L^2)*(rsr2*sr2/r)+0.5*log(L/U)/r+C);"
"U=r+sr2;"
"C=2*(1/or11/L)*step(sr2ror1);"
"L=max(or1, D);"
"D=abs(rsr2);"
"sr2 = scale2*or2;"
"or1 = radius10.009; or2 = radius20.009", CustomGBForce::ParticlePairNoExclusions);
custom>addComputedValue("B", "1/(1/ortanh(1*psi0.8*psi^2+4.85*psi^3)/radius);"
"psi=I*or; or=radius0.009", CustomGBForce::SingleParticle);
custom>addEnergyTerm("28.3919551*(radius+0.14)^2*(radius/B)^60.5*138.935456*(1/soluteDielectric1/solventDielectric)*q^2/B",
CustomGBForce::SingleParticle);
custom>addEnergyTerm("138.935456*(1/soluteDielectric1/solventDielectric)*q1*q2/f;"
"f=sqrt(r^2+B1*B2*exp(r^2/(4*B1*B2)))", CustomGBForce::ParticlePair);
It begins by defining three perparticle 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 perparticle 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(). This will have no effect on Contexts that already exist unless you call updateParametersInContext().
CustomGBForce 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, 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. In expressions for particle pair calculations, the names of perparticle 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 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 expressions.
def __init__  (  self,  
args  
) 
__init__(self) > CustomGBForce __init__(self, other) > CustomGBForce
Create a CustomGBForce.
def addComputedValue  (  self,  
name,  
expression,  
type  
) 
addComputedValue(self, name, expression, type) > int
Add a computed value to calculate for each particle.
name  (string) the name of the value 
expression  (string) 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 perparticle 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 perparticle 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  (ComputationType) the method to use for computing this value 
def addEnergyTerm  (  self,  
expression,  
type  
) 
addEnergyTerm(self, expression, type) > int
Add a term to the energy computation.
expression  (string) 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 perparticle 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 perparticle 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  (ComputationType) the method to use for computing this value 
def addExclusion  (  self,  
particle1,  
particle2  
) 
addExclusion(self, particle1, particle2) > int
Add a particle pair to the list of interactions that should be excluded.
particle1  (int) the index of the first particle in the pair 
particle2  (int) the index of the second particle in the pair 
def addFunction  (  self,  
name,  
values,  
min,  
max  
) 
addFunction(self, name, values, min, max) > int
Add a tabulated function that may appear in expressions.
def addGlobalParameter  (  self,  
name,  
defaultValue  
) 
addGlobalParameter(self, name, defaultValue) > int
Add a new global parameter that the interaction may depend on.
name  (string) the name of the parameter 
defaultValue  (double) the default value of the parameter 
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  (vector< double >) the list of parameters for the new particle 
def addPerParticleParameter  (  self,  
name  
) 
addPerParticleParameter(self, name) > int
Add a new perparticle parameter that the interaction may depend on.
name  (string) the name of the parameter 
def addTabulatedFunction  (  self,  
name,  
function  
) 
addTabulatedFunction(self, name, function) > int
Add a tabulated function that may appear in expressions.
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. 
def getComputedValueParameters  (  self,  
index  
) 
Get the properties of a computed value.
index  (int) the index of the computed value for which to get parameters 
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,  
index  
) 
Get the properties of a term to the energy computation.
index  (int) the index of the term for which to get parameters 
def getExclusionParticles  (  self,  
index  
) 
Get the particles in a pair whose interaction should be excluded.
index  (int) the index of the exclusion for which to get particle indices 
def getFunctionParameters  (  self,  
index  
) 
Get the parameters for a tabulated function that may appear in expressions.
def getGlobalParameterDefaultValue  (  self,  
index  
) 
getGlobalParameterDefaultValue(self, index) > double
Get the default value of a global parameter.
index  (int) the index of the parameter for which to get the default value 
def getGlobalParameterName  (  self,  
index  
) 
getGlobalParameterName(self, index) > std::string const &
Get the name of a global parameter.
index  (int) the index of the parameter for which to get the name 
def getNonbondedMethod  (  self  ) 
getNonbondedMethod(self) > OpenMM::CustomGBForce::NonbondedMethod
Get the method used for handling long range nonbonded interactions.
def getNumComputedValues  (  self  ) 
getNumComputedValues(self) > int
Get the number of perparticle 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 perparticle 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.
index  (int) the index of the particle for which to get parameters 
def getPerParticleParameterName  (  self,  
index  
) 
getPerParticleParameterName(self, index) > std::string const &
Get the name of a perparticle parameter.
index  (int) the index of the parameter for which to get the name 
def getTabulatedFunction  (  self,  
args  
) 
getTabulatedFunction(self, index) > TabulatedFunction getTabulatedFunction(self, index) > TabulatedFunction
Get a reference to a tabulated function that may appear in expressions.
index  (int) the index of the function to get 
def getTabulatedFunctionName  (  self,  
index  
) 
getTabulatedFunctionName(self, index) > std::string const &
Get the name of a tabulated function that may appear in expressions.
index  (int) the index of the function to get 
def setComputedValueParameters  (  self,  
index,  
name,  
expression,  
type  
) 
Set the properties of a computed value.
index  (int) the index of the computed value for which to set parameters 
name  (string) the name of the value 
expression  (string) 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 perparticle 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 perparticle 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  (ComputationType) the method to use for computing this value 
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.
distance  (double) the cutoff distance, measured in nm 
def setEnergyTermParameters  (  self,  
index,  
expression,  
type  
) 
Set the properties of a term to the energy computation.
index  (int) the index of the term for which to set parameters 
expression  (string) 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 perparticle 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 perparticle 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  (ComputationType) the method to use for computing this value 
def setExclusionParticles  (  self,  
index,  
particle1,  
particle2  
) 
Set the particles in a pair whose interaction should be excluded.
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 expressions.
def setGlobalParameterDefaultValue  (  self,  
index,  
defaultValue  
) 
Set the default value of a global parameter.
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.
index  (int) the index of the parameter for which to set the name 
name  (string) the name of the parameter 
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.
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 perparticle parameter.
index  (int) the index of the parameter for which to set the name 
name  (string) the name of the parameter 
def updateParametersInContext  (  self,  
context  
) 
Update the perparticle 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 perparticle parameters. All other aspects of the Force (such as the energy function) 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.
Reimplemented from Force.
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] 