CustomNonbondedForce
¶

class CustomNonbondedForce : public OpenMM::Force¶
This class implements nonbonded interactions between particles. Unlike NonbondedForce, the functional form of the interaction is completely customizable, and may involve arbitrary algebraic expressions and tabulated functions. It may depend on the distance between particles, as well as on arbitrary global and perparticle parameters. It also optionally supports periodic boundary conditions and cutoffs for long range interactions.
To use this class, create a CustomNonbondedForce object, passing an algebraic expression to the constructor that defines the interaction energy between each pair of particles. The expression may depend on r, the distance between the particles, as well as on any parameters you choose. Then call addPerParticleParameter() to define perparticle parameters, and addGlobalParameter() to define global parameters. The values of perparticle parameters are specified as part of the system definition, while values of global parameters may be modified during a simulation by calling Context::setParameter().
Next, call addParticle() once for each particle in the System to set the values of its perparticle parameters. 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().
CustomNonbondedForce also lets you specify “exclusions”, particular pairs of particles whose interactions should be omitted from force and energy calculations. This is most often used for particles that are bonded to each other.
As an example, the following code creates a CustomNonbondedForce that implements a 126 LennardJones potential:
CustomNonbondedForce* force = new CustomNonbondedForce("4*epsilon*((sigma/r)^12(sigma/r)^6); sigma=0.5*(sigma1+sigma2); epsilon=sqrt(epsilon1*epsilon2)");
This force depends on two parameters: sigma and epsilon. The following code defines these as perparticle parameters:
force>addPerParticleParameter("sigma"); force>addPerParticleParameter("epsilon");
The expression must be symmetric with respect to the two particles. It typically will only be evaluated once for each pair of particles, and no guarantee is made about which particle will be identified as “particle 1”. In the above example, the energy only depends on the products sigma1*sigma2 and epsilon1*epsilon2, both of which are unchanged if the labels 1 and 2 are reversed. In contrast, if it depended on the difference sigma1sigma2, the results would be undefined, because reversing the labels 1 and 2 would change the energy.
The energy also may depend on “computed values”. These are similar to perparticle parameters, but instead of being specified in advance, their values are computed based on global and perparticle parameters. For example, the following code uses a global parameter (lambda) to interpolate between two different sigma values for each particle (sigmaA and sigmaB).
CustomNonbondedForce* force = new CustomNonbondedForce("4*epsilon*((sigma/r)^12(sigma/r)^6); sigma=0.5*(sigma1+sigma2); epsilon=sqrt(epsilon1*epsilon2)"); force>addComputedValue("sigma", "(1lambda)*sigmaA + lambda*sigmaB"); force>addGlobalParameter("lambda", 0); force>addPerParticleParameter("sigmaA"); force>addPerParticleParameter("sigmaB"); force>addPerParticleParameter("epsilon");
You could, of course, embed the computation of sigma directly into the energy expression, but then it would need to be repeated for every interaction. By separating it out as a computed value, it only needs to be computed once for each particle instead of once for each interaction, thus saving computation time.
CustomNonbondedForce can operate in two modes. By default, it computes the interaction of every particle in the System with every other particle. Alternatively, you can restrict it to only a subset of particle pairs. To do this, specify one or more “interaction groups”. An interaction group consists of two sets of particles that should interact with each other. Every particle in the first set interacts with every particle in the second set. For example, you might use this feature to compute a solutesolvent interaction energy, while omitting all interactions between two solute atoms or two solvent atoms.
To create an interaction group, call addInteractionGroup(). You may add as many interaction groups as you want. Be aware of the following:
Exclusions are still taken into account, so the interactions between excluded pairs are omitted.
Likewise, a particle will never interact with itself, even if it appears in both sets of an interaction group.
If a particle pair appears in two different interaction groups, its interaction will be computed twice. This is sometimes useful, but be aware of it so you do not accidentally create unwanted duplicate interactions.
If you do not add any interaction groups to a CustomNonbondedForce, it operates in the default mode where every particle interacts with every other particle.
When using a cutoff, by default the interaction is sharply truncated at the cutoff distance. Optionally you can instead use a switching function to make the interaction smoothly go to zero over a finite distance range. To enable this, call setUseSwitchingFunction(). You must also call setSwitchingDistance() to specify the distance at which the interaction should begin to decrease. The switching distance must be less than the cutoff distance. Of course, you could also incorporate the switching function directly into your energy expression, but there are several advantages to keeping it separate. It makes your energy expression simpler to write and understand. It allows you to use the same energy expression with or without a cutoff. Also, when using a long range correction (see below), separating out the switching function allows the correction to be calculated more accurately.
Another optional feature of this class is to add a contribution to the energy which approximates the effect of all interactions beyond the cutoff in a periodic system. When running a simulation at constant pressure, this can improve the quality of the result. Call setUseLongRangeCorrection() to enable it.
Computing the long range correction takes negligible work in each time step, but it does require an expensive precomputation at the start of the simulation. Furthermore, that precomputation must be repeated every time a global parameter changes (or when you modify perparticle parameters by calling updateParametersInContext()). This means that if parameters change frequently, the long range correction can be very slow. For this reason, it is disabled by default.
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. The names of perparticle parameters have the suffix “1” or “2” appended to them to indicate the values for the two interacting particles. As seen in the above example, the 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 the expression.
Public Types

enum NonbondedMethod¶
This is an enumeration of the different methods that may be used for handling long range nonbonded forces.
Values:

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.

enumerator CutoffNonPeriodic¶
Interactions beyond the cutoff distance are ignored.

enumerator 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.

enumerator NoCutoff¶
Public Functions

explicit CustomNonbondedForce(const std::string &energy)¶
Create a CustomNonbondedForce.
 Parameters
energy – an algebraic expression giving the interaction energy between two particles as a function of r, the distance between them, as well as any global and perparticle parameters

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

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

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

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

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

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

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

inline int getNumInteractionGroups() const¶
Get the number of interaction groups that have been defined.

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

const std::string &getEnergyFunction() const¶
Get the algebraic expression that gives the interaction energy between two particles

void setEnergyFunction(const std::string &energy)¶
Set the algebraic expression that gives the interaction energy between two particles

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

bool getUseSwitchingFunction() const¶
Get whether a switching function is applied to the interaction. If the nonbonded method is set to NoCutoff, this option is ignored.

void setUseSwitchingFunction(bool use)¶
Set whether a switching function is applied to the interaction. If the nonbonded method is set to NoCutoff, this option is ignored.

double getSwitchingDistance() const¶
Get the distance at which the switching function begins to reduce the interaction. This must be less than the cutoff distance.

void setSwitchingDistance(double distance)¶
Set the distance at which the switching function begins to reduce the interaction. This must be less than the cutoff distance.

bool getUseLongRangeCorrection() const¶
Get whether to add a correction to the energy to compensate for the cutoff and switching function. This has no effect if periodic boundary conditions are not used.

void setUseLongRangeCorrection(bool use)¶
Set whether to add a correction to the energy to compensate for the cutoff and switching function. This has no effect if periodic boundary conditions are not used.

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 with addGlobalParameter().
 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

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 addExclusion(int particle1, int particle2)¶
Add a particle pair to the list of interactions that should be excluded.
In many cases, you can use createExclusionsFromBonds() rather than adding each exclusion explicitly.
 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

void createExclusionsFromBonds(const std::vector<std::pair<int, int>> &bonds, int bondCutoff)¶
Identify exclusions based on the molecular topology. Particles which are separated by up to a specified number of bonds are added as exclusions.
 Parameters
bonds – the set of bonds based on which to construct exclusions. Each element specifies the indices of two particles that are bonded to each other.
bondCutoff – pairs of particles that are separated by this many bonds or fewer are added to the list of exclusions

int addTabulatedFunction(const std::string &name, TabulatedFunction *function)¶
Add a tabulated function that may appear in the energy expression.
 Parameters
name – the name of the function as it appears in expressions
function – 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

const TabulatedFunction &getTabulatedFunction(int index) const¶
Get a const reference to a tabulated function that may appear in the energy expression.
 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 the energy expression.
 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 the energy expression.
 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 the energy expression.
 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 the energy expression.
 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 the energy expression.
 Deprecated:
This method exists only for backward compatibility. Use setTabulatedFunctionParameters() instead. If the specified function is not a Continuous1DFunction, this throws an exception.

int addComputedValue(const std::string &name, const std::string &expression)¶
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. It may depend on the values of perparticle and global parameters, but not one other computed values.
 Returns
the index of the computed value that was added

void getComputedValueParameters(int index, std::string &name, std::string &expression) 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. It may depend on the values of perparticle and global parameters, but not one other computed values.

void setComputedValueParameters(int index, const std::string &name, const std::string &expression)¶
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. It may depend on the values of perparticle and global parameters, but not one other computed values.

int addInteractionGroup(const std::set<int> &set1, const std::set<int> &set2)¶
Add an interaction group. An interaction will be computed between every particle in set1 and every particle in set2.
 Parameters
set1 – the first set of particles forming the interaction group
set2 – the second set of particles forming the interaction group
 Returns
the index of the interaction group that was added

void getInteractionGroupParameters(int index, std::set<int> &set1, std::set<int> &set2) const¶
Get the parameters for an interaction group.
 Parameters
index – the index of the interaction group for which to get parameters
set1 – [out] the first set of particles forming the interaction group
set2 – [out] the second set of particles forming the interaction group

void setInteractionGroupParameters(int index, const std::set<int> &set1, const std::set<int> &set2)¶
Set the parameters for an interaction group.
 Parameters
index – the index of the interaction group for which to set parameters
set1 – the first set of particles forming the interaction group
set2 – the second set of particles forming the interaction group

void updateParametersInContext(Context &context)¶
Update the perparticle 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 perparticle parameters and tabulated functions. All other aspects of the Force (the energy function, nonbonded method, cutoff distance, etc.) 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.

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