CustomGBForce¶

class
OpenMM::
CustomGBForce
¶ 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
When specifying a computed value or energy term, you provide an algebraic expression to evaluate and a
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 theSystem
energy.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
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 theSystem
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 theSystem
, or else an exception will be thrown when you try to create aContext
. After a particle has been added, you can modify its parameters by callingsetParticleParameters()
. This will have no effect on Contexts that already exist unless you callupdateParametersInContext()
.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 aContext
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, 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 aTabulatedFunction
object. That function can then appear in expressions.Methods
CustomGBForce
Create a CustomGBForce
.~CustomGBForce
getNumParticles
Get the number of particles for which force field parameters have been defined. getNumExclusions
Get the number of particle pairs whose interactions should be excluded. getNumPerParticleParameters
Get the number of perparticle parameters that the interaction depends on. getNumGlobalParameters
Get the number of global parameters that the interaction depends on. getNumEnergyParameterDerivatives
Get the number of global parameters with respect to which the derivative of the energy should be computed. getNumTabulatedFunctions
Get the number of tabulated functions that have been defined. getNumFunctions
Get the number of tabulated functions that have been defined. getNumComputedValues
Get the number of perparticle computed values the interaction depends on. getNumEnergyTerms
Get the number of terms in the energy computation. getNonbondedMethod
Get the method used for handling long range nonbonded interactions. setNonbondedMethod
Set the method used for handling long range nonbonded interactions. getCutoffDistance
Get the cutoff distance (in nm) being used for nonbonded interactions. setCutoffDistance
Set the cutoff distance (in nm) being used for nonbonded interactions. addPerParticleParameter
Add a new perparticle parameter that the interaction may depend on. getPerParticleParameterName
Get the name of a perparticle parameter. setPerParticleParameterName
Set the name of a perparticle parameter. addGlobalParameter
Add a new global parameter that the interaction may depend on. getGlobalParameterName
Get the name of a global parameter. setGlobalParameterName
Set the name of a global parameter. getGlobalParameterDefaultValue
Get the default value of a global parameter. setGlobalParameterDefaultValue
Set the default value of a global parameter. addEnergyParameterDerivative
Request that this Force
compute the derivative of its energy with respect to a global parameter.getEnergyParameterDerivativeName
Get the name of a global parameter with respect to which this Force
should compute the derivative of the energy.addParticle
Add the nonbonded force parameters for a particle. getParticleParameters
Get the nonbonded force parameters for a particle. setParticleParameters
Set the nonbonded force parameters for a particle. addComputedValue
Add a computed value to calculate for each particle. getComputedValueParameters
Get the properties of a computed value. setComputedValueParameters
Set the properties of a computed value. addEnergyTerm
Add a term to the energy computation. getEnergyTermParameters
Get the properties of a term to the energy computation. setEnergyTermParameters
Set the properties of a term to the energy computation. addExclusion
Add a particle pair to the list of interactions that should be excluded. getExclusionParticles
Get the particles in a pair whose interaction should be excluded. setExclusionParticles
Set the particles in a pair whose interaction should be excluded. addTabulatedFunction
Add a tabulated function that may appear in expressions. getTabulatedFunction
Get a const reference to a tabulated function that may appear in expressions. getTabulatedFunction
Get a reference to a tabulated function that may appear in expressions. getTabulatedFunctionName
Get the name of a tabulated function that may appear in expressions. addFunction
Add a tabulated function that may appear in expressions. getFunctionParameters
Get the parameters for a tabulated function that may appear in expressions. setFunctionParameters
Set the parameters for a tabulated function that may appear in expressions. updateParametersInContext
Update the perparticle parameters in a Context
to match those stored in thisForce
object.usesPeriodicBoundaryConditions
Returns whether or not this force makes use of periodic boundary conditions. Enum: NonbondedMethod
NoCutoff No cutoff is applied to nonbonded interactions. The full set of N^2 interactions is computed exactly. This necessarily means that periodic boundary conditions cannot be used. This is the default. CutoffNonPeriodic Interactions beyond the cutoff distance are ignored. CutoffPeriodic Periodic boundary conditions are used, so that each particle interacts only with the nearest periodic copy of each other particle. Interactions beyond the cutoff distance are ignored. Enum: ComputationType
SingleParticle The value is computed independently for each particle, based only on the parameters and computed values for that particle. ParticlePair The value is computed as a sum over all pairs of particles, except those which have been added as exclusions. ParticlePairNoExclusions The value is computed as a sum over all pairs of particles. Unlike ParticlePair, the list of exclusions is ignored and all pairs are included in the sum, even those marked as exclusions. 
CustomGBForce
()¶ Create a
CustomGBForce()
.

~CustomGBForce
()¶

int
getNumParticles
() const¶ Get the number of particles for which force field parameters have been defined.

int
getNumExclusions
() const¶ Get the number of particle pairs whose interactions should be excluded.

int
getNumPerParticleParameters
() const¶ Get the number of perparticle parameters that the interaction depends on.

int
getNumGlobalParameters
() const¶ Get the number of global parameters that the interaction depends on.

int
getNumEnergyParameterDerivatives
() const¶ Get the number of global parameters with respect to which the derivative of the energy should be computed.

int
getNumTabulatedFunctions
() const¶ Get the number of tabulated functions that have been defined.

int
getNumFunctions
() const¶ Get the number of tabulated functions that have been defined.
Deprecated
This method exists only for backward compatibility. Use
getNumTabulatedFunctions()
instead.

int
getNumComputedValues
() const¶ Get the number of perparticle computed values the interaction depends on.

int
getNumEnergyTerms
() const¶ Get the number of terms in the energy computation.

NonbondedMethod
getNonbondedMethod
() const¶ Get the method used for handling long range nonbonded interactions.

void
setNonbondedMethod
(NonbondedMethod method)¶ Set the method used for handling long range nonbonded interactions.

double
getCutoffDistance
() const¶ 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

void
setCutoffDistance
(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

int
addPerParticleParameter
(const std::string &name)¶ Add a new perparticle parameter that the interaction may depend on.
Parameters:  name – the name of the parameter
Returns: the index of the parameter that was added

const std::string &
getPerParticleParameterName
(int index) const¶ Get the name of a perparticle parameter.
Parameters:  index – the index of the parameter for which to get the name
Returns: the parameter name

void
setPerParticleParameterName
(int index, const std::string &name)¶ Set the name of a perparticle parameter.
Parameters:  index – the index of the parameter for which to set the name
 name – the name of the parameter

int
addGlobalParameter
(const std::string &name, double defaultValue)¶ 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 – the name of the parameter
 defaultValue – the default value of the parameter
Returns: the index of the parameter that was added

const std::string &
getGlobalParameterName
(int index) const¶ Get the name of a global parameter.
Parameters:  index – the index of the parameter for which to get the name
Returns: the parameter name

void
setGlobalParameterName
(int index, const std::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

double
getGlobalParameterDefaultValue
(int index) const¶ Get the default value of a global parameter.
Parameters:  index – the index of the parameter for which to get the default value
Returns: the parameter default value

void
setGlobalParameterDefaultValue
(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
 defaultValue – the default value of the parameter

void
addEnergyParameterDerivative
(const std::string &name)¶ Request that this
Force
compute the derivative of its energy with respect to a global parameter. The parameter must have already been added withaddGlobalParameter()
.Parameters:  name – the name of the parameter

const std::string &
getEnergyParameterDerivativeName
(int index) const¶ Get the name of a global parameter with respect to which this
Force
should compute the derivative of the energy.Parameters:  index – the index of the parameter derivative, between 0 and
getNumEnergyParameterDerivatives()
Returns: the parameter name  index – the index of the parameter derivative, between 0 and

int
addParticle
(const std::vector<double> ¶meters = std::vector< double >())¶ 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
Returns: the index of the particle that was added

void
getParticleParameters
(int index, std::vector<double> ¶meters) const¶ Get the nonbonded force parameters for a particle.
Parameters:  index – the index of the particle for which to get parameters
 parameters – [out] the list of parameters for the specified particle

void
setParticleParameters
(int index, const std::vector<double> ¶meters)¶ 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

int
addComputedValue
(const std::string &name, const std::string &expression, ComputationType type)¶ 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 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 – the method to use for computing this value

void
getComputedValueParameters
(int index, std::string &name, std::string &expression, ComputationType &type) const¶ Get the properties of a computed value.
Parameters:  index – the index of the computed value for which to get parameters
 name – [out] the name of the value
 expression – [out] 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 – [out] the method to use for computing this value

void
setComputedValueParameters
(int index, const std::string &name, const std::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 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 – the method to use for computing this value

int
addEnergyTerm
(const std::string &expression, ComputationType type)¶ 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 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 – the method to use for computing this value

void
getEnergyTermParameters
(int index, std::string &expression, ComputationType &type) const¶ Get the properties of a term to the energy computation.
Parameters:  index – the index of the term for which to get parameters
 expression – [out] 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 – [out] the method to use for computing this value

void
setEnergyTermParameters
(int index, const std::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 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 – the method to use for computing this value

int
addExclusion
(int particle1, int particle2)¶ 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
Returns: the index of the exclusion that was added

void
getExclusionParticles
(int index, int &particle1, int &particle2) const¶ 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 – [out] the index of the first particle in the pair
 particle2 – [out] the index of the second particle in the pair

void
setExclusionParticles
(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

int
addTabulatedFunction
(const std::string &name, TabulatedFunction *function)¶ Add a tabulated function that may appear in expressions.
Parameters:  name – the name of the function as it appears in expressions
 function – a
TabulatedFunction
object defining the function. TheTabulatedFunction
should have been created on the heap with the “new” operator. TheForce
takes over ownership of it, and deletes it when theForce
itself is deleted.
Returns: the index of the function that was added

const TabulatedFunction &
getTabulatedFunction
(int index) const¶ Get a const reference to a tabulated function that may appear in expressions.
Parameters:  index – the index of the function to get
Returns: the TabulatedFunction
object defining the function

TabulatedFunction &
getTabulatedFunction
(int index)¶ Get a reference to a tabulated function that may appear in expressions.
Parameters:  index – the index of the function to get
Returns: the TabulatedFunction
object defining the function

const std::string &
getTabulatedFunctionName
(int index) const¶ Get the name of a tabulated function that may appear in expressions.
Parameters:  index – the index of the function to get
Returns: the name of the function as it appears in expressions

int
addFunction
(const std::string &name, const std::vector<double> &values, double min, double max)¶ Add a tabulated function that may appear in expressions.
Deprecated
This method exists only for backward compatibility. Use
addTabulatedFunction()
instead.

void
getFunctionParameters
(int index, std::string &name, std::vector<double> &values, double &min, double &max) const¶ 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.

void
setFunctionParameters
(int index, const std::string &name, const std::vector<double> &values, double min, double 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.

void
updateParametersInContext
(Context &context)¶ Update the perparticle parameters in a
Context
to match those stored in thisForce
object. This method provides an efficient method to update certain parameters in an existingContext
without needing to reinitialize it. Simply callsetParticleParameters()
to modify this object’s parameters, then callupdateParametersInContext()
to copy them over to theContext
.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 theContext
. Also, this method cannot be used to add new particles, only to change the parameters of existing ones.

bool
usesPeriodicBoundaryConditions
() const¶ Returns whether or not this force makes use of periodic boundary conditions.
Returns: true if force uses PBC and false otherwise