`CustomHbondForce`¶

class CustomHbondForce : public OpenMM::Force ¶

This class supports a wide variety of energy functions used to represent hydrogen bonding. It computes interactions between “donor” particle groups and “acceptor” particle groups, where each group may include up to three particles. Typically a donor group consists of a hydrogen atom and the atoms it is bonded to, and an acceptor group consists of a negatively charged atom and the atoms it is bonded to.

We refer to the particles in a donor group as d1, d2 and d3, and the particles in an acceptor group as a1, a2, and a3. For each donor and each acceptor, CustomHbondForce evaluates a user supplied algebraic expression to determine the interaction energy. The expression may depend on arbitrary distances, angles, and dihedral angles defined by any of the six particles involved. The function distance(p1, p2) is the distance between the particles p1 and p2 (where “p1” and “p2” should be replaced by the names of the actual particles to calculate the distance between), angle(p1, p2, p3) is the angle formed by the three specified particles, and dihedral(p1, p2, p3, p4) is the dihedral angle formed by the four specified particles.

The expression also may involve tabulated functions, and may depend on arbitrary global, per-donor, and per-acceptor parameters. It also optionally supports periodic boundary conditions and cutoffs for long range interactions.

To use this class, create a CustomHbondForce object, passing an algebraic expression to the constructor that defines the interaction energy between each donor and acceptor. Then call addPerDonorParameter() to define per-donor parameters, addPerAcceptorParameter() to define per-acceptor parameters, and addGlobalParameter() to define global parameters. The values of per-donor and per-acceptor 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 addDonor() and addAcceptor() to define donors and acceptors and specify their parameter values. After a donor or acceptor has been added, you can modify its parameters by calling setDonorParameters() or setAcceptorParameters(). This will have no effect on Contexts that already exist unless you call updateParametersInContext().

CustomHbondForce also lets you specify “exclusions”, particular combinations of donors and acceptors 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 CustomHbondForce that implements a simple harmonic potential to keep the distance between a1 and d1, and the angle formed by a1-d1-d2, near ideal values:

CustomHbondForce* force = new CustomHbondForce("k*(distance(a1,d1)-r0)^2*(angle(a1,d1,d2)-theta0)^2");

This force depends on three parameters: k, r0, and theta0. The following code defines these as per-donor parameters:

force->addPerDonorParameter("k");
force->addPerDonorParameter("r0");
force->addPerDonorParameter("theta0");

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 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.

Public Functions

explicit CustomHbondForce(const std::string &energy)¶

Create a CustomHbondForce.

Parameters: energy – an algebraic expression giving the interaction energy between a donor and an acceptor as a function of inter-particle distances, angles, and dihedrals, as well as any global, per-donor, and per-acceptor parameters

inline int getNumDonors() const¶: Get the number of donors for which force field parameters have been defined.

inline int getNumAcceptors() const¶: Get the number of acceptors for which force field parameters have been defined.

inline int getNumExclusions() const¶: Get the number of donor-acceptor pairs whose interactions should be excluded.

inline int getNumPerDonorParameters() const¶: Get the number of per-donor parameters that the interaction depends on.

inline int getNumPerAcceptorParameters() const¶: Get the number of per-acceptor 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.

const std::string &getEnergyFunction() const¶: Get the algebraic expression that gives the interaction energy between a donor and an acceptor

void setEnergyFunction(const std::string &energy)¶: Set the algebraic expression that gives the interaction energy between a donor and an acceptor

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. All interactions for which the distance between d1 and a1 is greater than the cutoff will be ignored. 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. All interactions for which the distance between d1 and a1 is greater than the cutoff will be ignored. If the NonbondedMethod in use is NoCutoff, this value will have no effect.

Parameters: distance – the cutoff distance, measured in nm

int addPerDonorParameter(const std::string &name)¶

Add a new per-donor 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 &getPerDonorParameterName(int index) const¶

Get the name of a per-donor parameter.

Parameters: index – the index of the parameter for which to get the name
Returns: the parameter name

void setPerDonorParameterName(int index, const std::string &name)¶

Set the name of a per-donor parameter.

Parameters

index – the index of the parameter for which to set the name
name – the name of the parameter

int addPerAcceptorParameter(const std::string &name)¶

Add a new per-acceptor 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 &getPerAcceptorParameterName(int index) const¶

Get the name of a per-acceptor parameter.

Parameters: index – the index of the parameter for which to get the name
Returns: the parameter name

void setPerAcceptorParameterName(int index, const std::string &name)¶

Set the name of a per-acceptor 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

int addDonor(int d1, int d2, int d3, const std::vector<double> &parameters = std::vector<double>())¶

Add a donor group to the force

Parameters

d1 – the index of the first particle for this donor group
d2 – the index of the second particle for this donor group. If the group only includes one particle, this must be -1.
d3 – the index of the third particle for this donor group. If the group includes less than three particles, this must be -1.
parameters – the list of per-donor parameter values for the new donor

Returns

the index of the donor that was added

void getDonorParameters(int index, int &d1, int &d2, int &d3, std::vector<double> &parameters) const¶

Get the properties of a donor group.

Parameters

index – the index of the donor group to get
d1 – [out] the index of the first particle for this donor group
d2 – [out] the index of the second particle for this donor group. If the group only includes one particle, this will be -1.
d3 – [out] the index of the third particle for this donor group. If the group includes less than three particles, this will be -1.
parameters – [out] the list of per-donor parameter values for the donor

void setDonorParameters(int index, int d1, int d2, int d3, const std::vector<double> &parameters = std::vector<double>())¶

Set the properties of a donor group.

Parameters

index – the index of the donor group to set
d1 – the index of the first particle for this donor group
d2 – the index of the second particle for this donor group. If the group only includes one particle, this must be -1.
d3 – the index of the third particle for this donor group. If the group includes less than three particles, this must be -1.
parameters – the list of per-donor parameter values for the donor

int addAcceptor(int a1, int a2, int a3, const std::vector<double> &parameters = std::vector<double>())¶

Add an acceptor group to the force

Parameters

a1 – the index of the first particle for this acceptor group
a2 – the index of the second particle for this acceptor group. If the group only includes one particle, this must be -1.
a3 – the index of the third particle for this acceptor group. If the group includes less than three particles, this must be -1.
parameters – the list of per-acceptor parameter values for the new acceptor

Returns

the index of the acceptor that was added

void getAcceptorParameters(int index, int &a1, int &a2, int &a3, std::vector<double> &parameters) const¶

Get the properties of an acceptor group.

Parameters

index – the index of the acceptor group to get
a1 – [out] the index of the first particle for this acceptor group
a2 – [out] the index of the second particle for this acceptor group. If the group only includes one particle, this will be -1.
a3 – [out] the index of the third particle for this acceptor group. If the group includes less than three particles, this will be -1.
parameters – [out] the list of per-acceptor parameter values for the acceptor

void setAcceptorParameters(int index, int a1, int a2, int a3, const std::vector<double> &parameters = std::vector<double>())¶

Set the properties of an acceptor group.

Parameters

index – the index of the acceptor group to set
a1 – the index of the first particle for this acceptor group
a2 – the index of the second particle for this acceptor group. If the group only includes one particle, this must be -1.
a3 – the index of the third particle for this acceptor group. If the group includes less than three particles, this must be -1.
parameters – the list of per-acceptor parameter values for the acceptor

int addExclusion(int donor, int acceptor)¶

Add a donor-acceptor pair to the list of interactions that should be excluded.

Parameters

donor – the index of the donor to exclude
acceptor – the index of the acceptor to exclude

Returns

the index of the exclusion that was added

void getExclusionParticles(int index, int &donor, int &acceptor) const¶

Get the donor and acceptor in a pair whose interaction should be excluded.

Parameters

index – the index of the exclusion for which to get donor and acceptor indices
donor – [out] the index of the donor
acceptor – [out] the index of the acceptor

void setExclusionParticles(int index, int donor, int acceptor)¶

Get the donor and acceptor in a pair whose interaction should be excluded.

Parameters

index – the index of the exclusion for which to get donor and acceptor indices
donor – the index of the donor
acceptor – the index of the acceptor

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.

void updateParametersInContext(Context &context)¶

Update the per-donor and per-acceptor 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 setDonorParameters() and setAcceptorParameters() 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-donor and per-acceptor 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. The set of particles involved in a donor or acceptor cannot be changed, nor can new donors or acceptors be added. 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

CustomHbondForce¶

`CustomHbondForce`¶