CustomGBForce¶
- class openmm.openmm.CustomGBForce(*args)¶
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:
Single Particle: The expression is evaluated once for each particle in the System. In the case of a computed value, this means the value for a particle depends only on other properties of that particle (its position, parameters, and other computed values). In the case of an energy term, it means each particle makes an independent contribution to the System energy.
Particle Pairs: The expression is evaluated for every pair of particles in the system. In the case of a computed value, the value for a particular particle is calculated by pairing it with every other particle in the system, evaluating the expression for each pair, and summing them. For an energy term, each particle pair makes an independent contribution to the System energy. (Note that energy terms are assumed to be symmetric with respect to the two interacting particles, and therefore are evaluated only once per pair. In contrast, expressions for computed values need not be symmetric and therefore are calculated twice for each pair: once when calculating the value for the first particle, and again when calculating the value for the second particle.)
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(). 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.
This class also has the ability to compute derivatives of the potential energy with respect to global parameters. Call addEnergyParameterDerivative() to request that the derivative with respect to a particular parameter be computed. You can then query its value in a Context by calling getState() on it.
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, atan2, 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 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 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.
- __init__(self) → CustomGBForce¶
- __init__(self, other) → CustomGBForce
Create a CustomGBForce.
Methods
__init__
(-> CustomGBForce)Create a CustomGBForce.
addComputedValue
(self, name, expression, type)Add a computed value to calculate for each particle.
addEnergyParameterDerivative
(self, name)Request that this Force compute the derivative of its energy with respect to a global parameter.
addEnergyTerm
(self, expression, type)Add a term to the energy computation.
addExclusion
(self, particle1, particle2)Add a particle pair to the list of interactions that should be excluded.
addFunction
(self, name, values, min, max)Add a tabulated function that may appear in expressions.
addGlobalParameter
(self, name, defaultValue)Add a new global parameter that the interaction may depend on.
addParticle
(self[, parameters])Add the nonbonded force parameters for a particle.
addPerParticleParameter
(self, name)Add a new per-particle parameter that the interaction may depend on.
addTabulatedFunction
(self, name, function)Add a tabulated function that may appear in expressions.
getComputedValueParameters
(self, index)Get the properties of a computed value.
getCutoffDistance
(self)Get the cutoff distance (in nm) being used for nonbonded interactions.
getEnergyParameterDerivativeName
(self, index)Get the name of a global parameter with respect to which this Force should compute the derivative of the energy.
getEnergyTermParameters
(self, index)Get the properties of a term to the energy computation.
getExclusionParticles
(self, index)Get the particles in a pair whose interaction should be excluded.
getForceGroup
(self)Get the force group this Force belongs to.
getFunctionParameters
(self, index)Get the parameters for a tabulated function that may appear in expressions.
getGlobalParameterDefaultValue
(self, index)Get the default value of a global parameter.
getGlobalParameterName
(self, index)Get the name of a global parameter.
getName
(self)Get the name of this Force.
getNonbondedMethod
(self)Get the method used for handling long range nonbonded interactions.
getNumComputedValues
(self)Get the number of per-particle computed values the interaction depends on.
Get the number of global parameters with respect to which the derivative of the energy should be computed.
getNumEnergyTerms
(self)Get the number of terms in the energy computation.
getNumExclusions
(self)Get the number of particle pairs whose interactions should be excluded.
getNumFunctions
(self)Get the number of tabulated functions that have been defined.
getNumGlobalParameters
(self)Get the number of global parameters that the interaction depends on.
getNumParticles
(self)Get the number of particles for which force field parameters have been defined.
Get the number of per-particle parameters that the interaction depends on.
getNumTabulatedFunctions
(self)Get the number of tabulated functions that have been defined.
getParticleParameters
(self, index)Get the nonbonded force parameters for a particle.
getPerParticleParameterName
(self, index)Get the name of a per-particle parameter.
getTabulatedFunction
(-> TabulatedFunction)Get a reference to a tabulated function that may appear in expressions.
getTabulatedFunctionName
(self, index)Get the name of a tabulated function that may appear in expressions.
setComputedValueParameters
(self, index, …)Set the properties of a computed value.
setCutoffDistance
(self, distance)Set the cutoff distance (in nm) being used for nonbonded interactions.
setEnergyTermParameters
(self, index, …)Set the properties of a term to the energy computation.
setExclusionParticles
(self, index, …)Set the particles in a pair whose interaction should be excluded.
setForceGroup
(self, group)Set the force group this Force belongs to.
setFunctionParameters
(self, index, name, …)Set the parameters for a tabulated function that may appear in expressions.
setGlobalParameterDefaultValue
(self, index, …)Set the default value of a global parameter.
setGlobalParameterName
(self, index, name)Set the name of a global parameter.
setName
(self, name)Set the name of this Force.
setNonbondedMethod
(self, method)Set the method used for handling long range nonbonded interactions.
setParticleParameters
(self, index, parameters)Set the nonbonded force parameters for a particle.
setPerParticleParameterName
(self, index, name)Set the name of a per-particle parameter.
updateParametersInContext
(self, context)Update the per-particle parameters and tabulated functions in a Context to match those stored in this Force object.
Returns whether or not this force makes use of periodic boundary conditions.
Attributes
CutoffNonPeriodic
CutoffPeriodic
NoCutoff
ParticlePair
ParticlePairNoExclusions
SingleParticle
The membership flag
- property thisown¶
The membership flag
- getNumParticles(self) → int¶
Get the number of particles for which force field parameters have been defined.
- getNumExclusions(self) → int¶
Get the number of particle pairs whose interactions should be excluded.
- getNumPerParticleParameters(self) → int¶
Get the number of per-particle parameters that the interaction depends on.
- getNumGlobalParameters(self) → int¶
Get the number of global parameters that the interaction depends on.
- getNumEnergyParameterDerivatives(self) → int¶
Get the number of global parameters with respect to which the derivative of the energy should be computed.
- getNumTabulatedFunctions(self) → int¶
Get the number of tabulated functions that have been defined.
- getNumFunctions(self) → int¶
Get the number of tabulated functions that have been defined.
Deprecated
This method exists only for backward compatibility. Use getNumTabulatedFunctions() instead.
- getNumComputedValues(self) → int¶
Get the number of per-particle computed values the interaction depends on.
- getNumEnergyTerms(self) → int¶
Get the number of terms in the energy computation.
- getNonbondedMethod(self) → OpenMM::CustomGBForce::NonbondedMethod¶
Get the method used for handling long range nonbonded interactions.
- setNonbondedMethod(self, method)¶
Set the method used for handling long range nonbonded interactions.
- 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
the cutoff distance, measured in nm
- Return type
double
- 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
- 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
the index of the parameter that was added
- Return type
int
- 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
the parameter name
- Return type
string
- 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
- addGlobalParameter(self, name, defaultValue) → int¶
Add a new global parameter that the interaction may depend on. The default value provided to this method is the initial value of the parameter in newly created Contexts. You can change the value at any time by calling setParameter() on the Context.
- Parameters
name (string) – the name of the parameter
defaultValue (double) – the default value of the parameter
- Returns
the index of the parameter that was added
- Return type
int
- 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
the parameter name
- Return type
string
- 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
- 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
the parameter default value
- Return type
double
- 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
- addEnergyParameterDerivative(self, name)¶
Request that this Force compute the derivative of its energy with respect to a global parameter. The parameter must have already been added with addGlobalParameter().
- Parameters
name (string) – the name of the parameter
- getEnergyParameterDerivativeName(self, index) → std::string const &¶
Get the name of a global parameter with respect to which this Force should compute the derivative of the energy.
- Parameters
index (int) – the index of the parameter derivative, between 0 and getNumEnergyParameterDerivatives()
- Returns
the parameter name
- Return type
string
- addParticle(self, parameters=std::vector< double >()) → 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
the index of the particle that was added
- Return type
int
- 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
parameters – the list of parameters for the specified particle
- Return type
vector< double >
- 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
- addComputedValue(self, name, expression, type) → int¶
Add a computed value to calculate for each particle.
- 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 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 (ComputationType) – the method to use for computing this value
- getComputedValueParameters(self, index)¶
Get the properties of a computed value.
- Parameters
index (int) – the index of the computed value for which to get parameters
- Returns
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 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 (ComputationType) – the method to use for computing this value
- setComputedValueParameters(self, index, name, expression, type)¶
Set the properties of a computed value.
- Parameters
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 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 (ComputationType) – the method to use for computing this value
- addEnergyTerm(self, expression, type) → int¶
Add a term to the energy computation.
- 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 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 (ComputationType) – the method to use for computing this value
- getEnergyTermParameters(self, index)¶
Get the properties of a term to the energy computation.
- Parameters
index (int) – the index of the term for which to get parameters
- Returns
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 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 (ComputationType) – the method to use for computing this value
- setEnergyTermParameters(self, index, expression, type)¶
Set the properties of a term to the energy computation.
- Parameters
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 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 (ComputationType) – the method to use for computing this value
- addExclusion(self, particle1, particle2) → int¶
Add a particle pair to the list of interactions that should be excluded.
- Parameters
particle1 (int) – the index of the first particle in the pair
particle2 (int) – the index of the second particle in the pair
- Returns
the index of the exclusion that was added
- Return type
int
- 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
particle1 (int) – the index of the first particle in the pair
particle2 (int) – the index of the second particle in the pair
- 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
- addTabulatedFunction(self, name, function) → int¶
Add a tabulated function that may appear in expressions.
- 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
the index of the function that was added
- Return type
int
- getTabulatedFunction(self, index) → TabulatedFunction¶
- getTabulatedFunction(self, index) → TabulatedFunction
Get a reference to a tabulated function that may appear in expressions.
- Parameters
index (int) – the index of the function to get
- Returns
the TabulatedFunction object defining the function
- Return type
- getTabulatedFunctionName(self, index) → std::string const &¶
Get the name of a tabulated function that may appear in expressions.
- Parameters
index (int) – the index of the function to get
- Returns
the name of the function as it appears in expressions
- Return type
string
- addFunction(self, name, values, min, max) → int¶
Add a tabulated function that may appear in expressions.
Deprecated
This method exists only for backward compatibility. Use addTabulatedFunction() instead.
- getFunctionParameters(self, index)¶
Get the parameters for a tabulated function that may appear in expressions.
Deprecated
This method exists only for backward compatibility. Use getTabulatedFunctionParameters() instead. If the specified function is not a Continuous1DFunction, this throws an exception.
- setFunctionParameters(self, index, name, values, min, max)¶
Set the parameters for a tabulated function that may appear in expressions.
Deprecated
This method exists only for backward compatibility. Use setTabulatedFunctionParameters() instead. If the specified function is not a Continuous1DFunction, this throws an exception.
- updateParametersInContext(self, context)¶
Update the per-particle parameters and tabulated functions 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 and tabulated functions. 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. While the tabulated values of a function can change, everything else about it (its dimensions, the data range) must not be changed.
- usesPeriodicBoundaryConditions(self) → bool¶
Returns whether or not this force makes use of periodic boundary conditions.
- Returns
true if force uses PBC and false otherwise
- Return type
bool
- getForceGroup(self) → int¶
Get the force group this Force belongs to.
- getName(self) → std::string const &¶
Get the name of this Force. This is an arbitrary, user modifiable identifier. By default it equals the class name, but you can change it to anything useful.
- setForceGroup(self, group)¶
Set the force group this Force belongs to.
- Parameters
group (int) – the group index. Legal values are between 0 and 31 (inclusive).
- setName(self, name)¶
Set the name of this Force. This is an arbitrary, user modifiable identifier. By default it equals the class name, but you can change it to anything useful.