CustomGBForce Class Reference

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

#include <CustomGBForce.h>

Inheritance diagram for CustomGBForce:
Force

List of all members.

Classes

class  ComputationInfo
 This is an internal class used to record information about a computed value or energy term.
class  ExclusionInfo
 This is an internal class used to record information about an exclusion.
class  FunctionInfo
 This is an internal class used to record information about a tabulated function.
class  GlobalParameterInfo
 This is an internal class used to record information about a global parameter.
class  ParticleInfo
 This is an internal class used to record information about a particle.
class  PerParticleParameterInfo
 This is an internal class used to record information about a per-particle parameter.

Public Types

enum  NonbondedMethod { NoCutoff = 0, CutoffNonPeriodic = 1, CutoffPeriodic = 2 }
 

This is an enumeration of the different methods that may be used for handling long range nonbonded forces.

More...
enum  ComputationType { SingleParticle = 0, ParticlePair = 1, ParticlePairNoExclusions = 2 }
 

This is an enumeration of the different ways in which a computed value or energy term can be calculated.

More...

Public Member Functions

 CustomGBForce ()
 Create a 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 per-particle parameters that the interaction depends on.
int getNumGlobalParameters () const
 Get the number of global parameters that the interaction depends on.
int getNumFunctions () const
 Get the number of tabulated functions that have been defined.
int getNumComputedValues () const
 Get the number of per-particle 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.
void setCutoffDistance (double distance)
 Set the cutoff distance (in nm) being used for nonbonded interactions.
int addPerParticleParameter (const std::string &name)
 Add a new per-particle parameter that the interaction may depend on.
const std::string & getPerParticleParameterName (int index) const
 Get the name of a per-particle parameter.
void setPerParticleParameterName (int index, const std::string &name)
 Set the name of a per-particle parameter.
int addGlobalParameter (const std::string &name, double defaultValue)
 Add a new global parameter that the interaction may depend on.
const std::string & getGlobalParameterName (int index) const
 Get the name of a global parameter.
void setGlobalParameterName (int index, const std::string &name)
 Set the name of a global parameter.
double getGlobalParameterDefaultValue (int index) const
 Get the default value of a global parameter.
void setGlobalParameterDefaultValue (int index, double defaultValue)
 Set the default value of a global parameter.
int addParticle (const std::vector< double > &parameters)
 Add the nonbonded force parameters for a particle.
void getParticleParameters (int index, std::vector< double > &parameters) const
 Get the nonbonded force parameters for a particle.
void setParticleParameters (int index, const std::vector< double > &parameters)
 Set the nonbonded force parameters for a particle.
int addComputedValue (const std::string &name, const std::string &expression, ComputationType type)
 Add a computed value to calculate for each particle.
void getComputedValueParameters (int index, std::string &name, std::string &expression, ComputationType &type) const
 Get the properties of a computed value.
void setComputedValueParameters (int index, const std::string &name, const std::string &expression, ComputationType type)
 Set the properties of a computed value.
int addEnergyTerm (const std::string &expression, ComputationType type)
 Add a term to the energy computation.
void getEnergyTermParameters (int index, std::string &expression, ComputationType &type) const
 Get the properties of a term to the energy computation.
void setEnergyTermParameters (int index, const std::string &expression, ComputationType type)
 Set the properties of a term to the energy computation.
int addExclusion (int particle1, int particle2)
 Add a particle pair to the list of interactions that should be excluded.
void getExclusionParticles (int index, int &particle1, int &particle2) const
 Get the particles in a pair whose interaction should be excluded.
void setExclusionParticles (int index, int particle1, int particle2)
 Set the particles in a pair whose interaction should be excluded.
int addFunction (const std::string &name, const std::vector< double > &values, double min, double max, bool interpolating)
 Add a tabulated function that may appear in the energy expression.
void getFunctionParameters (int index, std::string &name, std::vector< double > &values, double &min, double &max, bool &interpolating) const
 Get the parameters for a tabulated function that may appear in the energy expression.
void setFunctionParameters (int index, const std::string &name, const std::vector< double > &values, double min, double max, bool interpolating)
 Set the parameters for a tabulated function that may appear in algebraic expressions.

Protected Member Functions

ForceImpl * createImpl ()
 When a Context is created, it invokes this method on each Force in the System.

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=step(or1-D)*or1+(1-step(or1-D))*D;"
                               "D=step(r-sr2)*(r-sr2)+(1-step(r-sr2))*(sr2-r);"
                               "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, 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 an interpolating or approximating spline is created from them. That function can then appear in expressions.

Member Enumeration Documentation

enum ComputationType

This is an enumeration of the different ways in which a computed value or energy term can be calculated.

Enumerator:
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.

enum NonbondedMethod

This is an enumeration of the different methods that may be used for handling long range nonbonded forces.

Enumerator:
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.

Constructor & Destructor Documentation

CustomGBForce (  ) 

Create a CustomGBForce.

Member Function Documentation

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 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
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 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
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
int addFunction ( const std::string &  name,
const std::vector< double > &  values,
double  min,
double  max,
bool  interpolating 
)

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
interpolating if true, an interpolating (Catmull-Rom) spline will be used to represent the function. If false, an approximating spline (B-spline) will be used.
Returns:
the index of the function that was added
int addGlobalParameter ( const std::string &  name,
double  defaultValue 
)

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
Returns:
the index of the parameter that was added
int addParticle ( const std::vector< double > &  parameters  ) 

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
int addPerParticleParameter ( const std::string &  name  ) 

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

Parameters:
name the name of the parameter
Returns:
the index of the parameter that was added
ForceImpl* createImpl (  )  [protected, virtual]

When a Context is created, it invokes this method on each Force in the System.

It should create a new ForceImpl object which can be used by the context for calculating forces. The ForceImpl will be deleted automatically when the Context is deleted.

Implements Force.

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 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 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
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 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 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 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
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 the index of the first particle in the pair
particle2 the index of the second particle in the pair
void getFunctionParameters ( int  index,
std::string &  name,
std::vector< double > &  values,
double &  min,
double &  max,
bool &  interpolating 
) const

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
interpolating if true, an interpolating (Catmull-Rom) spline will be used to represent the function. If false, an approximating spline (B-spline) will be used.
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
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
NonbondedMethod getNonbondedMethod (  )  const

Get the method used for handling long range nonbonded interactions.

int getNumComputedValues (  )  const [inline]

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

int getNumEnergyTerms (  )  const [inline]

Get the number of terms in the energy computation.

int getNumExclusions (  )  const [inline]

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

int getNumFunctions (  )  const [inline]

Get the number of tabulated functions that have been defined.

int getNumGlobalParameters (  )  const [inline]

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

int getNumParticles (  )  const [inline]

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

int getNumPerParticleParameters (  )  const [inline]

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

void getParticleParameters ( int  index,
std::vector< double > &  parameters 
) const

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
const std::string& getPerParticleParameterName ( int  index  )  const

Get the name of a per-particle parameter.

Parameters:
index the index of the parameter for which to get the name
Returns:
the parameter name
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 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
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
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 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
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
void setFunctionParameters ( int  index,
const std::string &  name,
const std::vector< double > &  values,
double  min,
double  max,
bool  interpolating 
)

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
interpolating if true, an interpolating (Catmull-Rom) spline will be used to represent the function. If false, an approximating spline (B-spline) will be used.
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
name the default value of the parameter
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
void setNonbondedMethod ( NonbondedMethod  method  ) 

Set the method used for handling long range nonbonded interactions.

void setParticleParameters ( int  index,
const std::vector< double > &  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
void setPerParticleParameterName ( int  index,
const std::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
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