CustomHbondForce

class OpenMM::CustomHbondForce

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, 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.

Methods

CustomHbondForce Create a CustomHbondForce.
~CustomHbondForce
getNumDonors Get the number of donors for which force field parameters have been defined.
getNumAcceptors Get the number of acceptors for which force field parameters have been defined.
getNumExclusions Get the number of donor-acceptor pairs whose interactions should be excluded.
getNumPerDonorParameters Get the number of per-donor parameters that the interaction depends on.
getNumPerAcceptorParameters Get the number of per-acceptor parameters that the interaction depends on.
getNumGlobalParameters Get the number of global parameters that the interaction depends on.
getNumTabulatedFunctions Get the number of tabulated functions that have been defined.
getNumFunctions Get the number of tabulated functions that have been defined.
getEnergyFunction Get the algebraic expression that gives the interaction energy between a donor and an acceptor
setEnergyFunction Set the algebraic expression that gives the interaction energy between a donor and an acceptor
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.
setCutoffDistance Set the cutoff distance (in nm) being used.
addPerDonorParameter Add a new per-donor parameter that the interaction may depend on.
getPerDonorParameterName Get the name of a per-donor parameter.
setPerDonorParameterName Set the name of a per-donor parameter.
addPerAcceptorParameter Add a new per-acceptor parameter that the interaction may depend on.
getPerAcceptorParameterName Get the name of a per-acceptor parameter.
setPerAcceptorParameterName Set the name of a per-acceptor 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.
addDonor Add a donor group to the force
getDonorParameters Get the properties of a donor group.
setDonorParameters Set the properties of a donor group.
addAcceptor Add an acceptor group to the force
getAcceptorParameters Get the properties of an acceptor group.
setAcceptorParameters Set the properties of an acceptor group.
addExclusion Add a donor-acceptor pair to the list of interactions that should be excluded.
getExclusionParticles Get the donor and acceptor in a pair whose interaction should be excluded.
setExclusionParticles Get the donor and acceptor in a pair whose interaction should be excluded.
addTabulatedFunction Add a tabulated function that may appear in the energy expression.
getTabulatedFunction Get a const reference to a tabulated function that may appear in the energy expression.
getTabulatedFunction Get a reference to a tabulated function that may appear in the energy expression.
getTabulatedFunctionName Get the name of a tabulated function that may appear in the energy expression.
addFunction Add a tabulated function that may appear in the energy expression.
getFunctionParameters Get the parameters for a tabulated function that may appear in the energy expression.
setFunctionParameters Set the parameters for a tabulated function that may appear in the energy expression.
updateParametersInContext Update the per-donor and per-acceptor parameters in a Context to match those stored in this Force 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.
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
~CustomHbondForce()
int getNumDonors() const

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

int getNumAcceptors() const

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

int getNumExclusions() const

Get the number of donor-acceptor pairs whose interactions should be excluded.

int getNumPerDonorParameters() const

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

int getNumPerAcceptorParameters() const

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

int getNumGlobalParameters() const

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

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.

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 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. 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.

bool usesPeriodicBoundaryConditions() const

Returns whether or not this force makes use of periodic boundary conditions.

Returns:true if force uses PBC and false otherwise