CustomCompoundBondForce

class CustomCompoundBondForce : public OpenMM::Force

This class supports a wide variety of bonded interactions. It defines a “bond” as a single energy term that depends on the positions of a fixed set of particles. The number of particles involved in a bond, and how the energy depends on their positions, is configurable. It may depend on the positions of individual particles, the distances between pairs of particles, the angles formed by sets of three particles, and the dihedral angles formed by sets of four particles.

We refer to the particles in a bond as p1, p2, p3, etc. For each bond, CustomCompoundBondForce evaluates a user supplied algebraic expression to determine the interaction energy. The expression may depend on the following variables and functions:

  • x1, y1, z1, x2, y2, z2, etc.: The x, y, and z coordinates of the particle positions. For example, x1 is the x coordinate of particle p1, and y3 is the y coordinate of particle p3.

  • distance(p1, p2): the distance between particles p1 and p2 (where “p1” and “p2” may be replaced by the names of whichever particles you want to calculate the distance between).

  • angle(p1, p2, p3): the angle formed by the three specified particles.

  • dihedral(p1, p2, p3, p4): the dihedral angle formed by the four specified particles, guaranteed to be in the range [-pi,+pi].

The expression also may involve tabulated functions, and may depend on arbitrary global and per-bond parameters.

To use this class, create a CustomCompoundBondForce object, passing an algebraic expression to the constructor that defines the interaction energy of each bond. Then call addPerBondParameter() to define per-bond parameters and addGlobalParameter() to define global parameters. The values of per-bond 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 addBond() to define bonds and specify their parameter values. After a bond has been added, you can modify its parameters by calling setBondParameters(). This will have no effect on Contexts that already exist unless you call updateParametersInContext().

As an example, the following code creates a CustomCompoundBondForce that implements a Urey-Bradley potential. This is an interaction between three particles that depends on the angle formed by p1-p2-p3, and on the distance between p1 and p3.

CustomCompoundBondForce* force = new CustomCompoundBondForce(3, "0.5*(kangle*(angle(p1,p2,p3)-theta0)^2+kbond*(distance(p1,p3)-r0)^2)");

This force depends on four parameters: kangle, kbond, theta0, and r0. The following code defines these as per-bond parameters:

force->addPerBondParameter("kangle");
force->addPerBondParameter("kbond");
force->addPerBondParameter("theta0");
force->addPerBondParameter("r0");

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.

This class also supports the functions pointdistance(x1, y1, z1, x2, y2, z2), pointangle(x1, y1, z1, x2, y2, z2, x3, y3, z3), and pointdihedral(x1, y1, z1, x2, y2, z2, x3, y3, z3, x4, y4, z4). These functions are similar to distance(), angle(), and dihedral(), but the arguments are the coordinates of points to perform the calculation based on rather than the names of particles. This enables more flexible geometric calculations. For example, the following computes the distance from particle p1 to the midpoint between particles p2 and p3.

CustomCompoundBondForce* force = new CustomCompoundBondForce(3, "pointdistance(x1, y1, z1, (x2+x3)/2, (y2+y3)/2, (z2+z3)/2)");

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 Functions

explicit CustomCompoundBondForce(int numParticles, const std::string &energy)

Create a CustomCompoundBondForce.

Parameters

  • numParticles – the number of particles used to define each bond

  • energy – an algebraic expression giving the interaction energy of each bond as a function of particle positions, inter-particle distances, angles, and dihedrals, and any global and per-bond parameters

inline int getNumParticlesPerBond() const

Get the number of particles used to define each bond.

inline int getNumBonds() const

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

inline int getNumPerBondParameters() const

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

inline int getNumGlobalParameters() const

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

inline int getNumEnergyParameterDerivatives() const

Get the number of global parameters with respect to which the derivative of the energy should be computed.

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 of each bond

void setEnergyFunction(const std::string &energy)

Set the algebraic expression that gives the interaction energy of each bond

int addPerBondParameter(const std::string &name)

Add a new per-bond 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 &getPerBondParameterName(int index) const

Get the name of a per-bond parameter.

Parameters

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

Returns

the parameter name

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

Set the name of a per-bond 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 addBond(const std::vector<int> &particles, const std::vector<double> &parameters = std::vector<double>())

Add a bond to the force

Parameters

  • particles – the indices of the particles the bond depends on

  • parameters – the list of per-bond parameter values for the new bond

Returns

the index of the bond that was added

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

Get the properties of a bond.

Parameters

  • index – the index of the bond to get

  • particles – [out] the indices of the particles in the bond

  • parameters – [out] the list of per-bond parameter values for the bond

void setBondParameters(int index, const std::vector<int> &particles, const std::vector<double> &parameters = std::vector<double>())

Set the properties of a bond.

Parameters

  • index – the index of the bond to set

  • particles – the indices of the particles in the bond

  • parameters – the list of per-bond parameter values for the bond

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. Call getFunctionParameters() on the TabulatedFunction object 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. Call setFunctionParameters() on the TabulatedFunction object instead. If the specified function is not a Continuous1DFunction, this throws an exception.

void updateParametersInContext(Context &context)

Update the per-bond 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 setBondParameters() 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-bond parameters and tabulated functions. All other aspects of the Force (such as the energy function) are unaffected and can only be changed by reinitializing the Context. The set of particles involved in a bond cannot be changed, nor can new bonds be added. Also, while the tabulated values of a function can change, everything else about it (its dimensions, the data range) must not be changed.

void setUsesPeriodicBoundaryConditions(bool periodic)

Set whether this force should apply periodic boundary conditions when calculating displacements. Usually this is not appropriate for bonded forces, but there are situations when it can be useful.

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