CustomBondForce¶

class OpenMM::CustomBondForce¶

This class implements bonded interactions between pairs of particles. Unlike HarmonicBondForce, the functional form of the interaction is completely customizable, and may involve arbitrary algebraic expressions. It may depend on the distance between particles, as well as on arbitrary global and per-bond parameters.

To use this class, create a CustomBondForce() object, passing an algebraic expression to the constructor that defines the interaction energy between each pair of bonded particles. The expression may depend on r, the distance between the particles, as well as on any parameters you choose. 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(). Finally, call addBond() once for each bond. 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 CustomBondForce() that implements a harmonic potential:

CustomBondForce* force = new CustomBondForce("0.5*k*(r-r0)^2");

This force depends on two parameters: the spring constant k and equilibrium distance r0. The following code defines these parameters:

force->addPerBondParameter("k");
force->addPerBondParameter("r0");

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.

Methods

`CustomBondForce()`	Create a `CustomBondForce()`.
`getNumBonds()`	Get the number of bonds for which force field parameters have been defined.
`getNumPerBondParameters()`	Get the number of per-bond parameters that the interaction depends on.
`getNumGlobalParameters()`	Get the number of global parameters that the interaction depends on.
`getEnergyFunction()`	Get the algebraic expression that gives the interaction energy for each bond
`setEnergyFunction()`	Set the algebraic expression that gives the interaction energy for each bond
`addPerBondParameter()`	Add a new per-bond parameter that the interaction may depend on.
`getPerBondParameterName()`	Get the name of a per-bond parameter.
`setPerBondParameterName()`	Set the name of a per-bond 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.
`addBond()`	Add a bond term to the force field.
`getBondParameters()`	Get the force field parameters for a bond term.
`setBondParameters()`	Set the force field parameters for a bond term.
`updateParametersInContext()`	Update the per-bond 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.

CustomBondForce(const std::string &energy)¶

Create a CustomBondForce().

Parameters:

energy – an algebraic expression giving the interaction energy between two bonded particles as a function of r, the distance between them

int getNumBonds() const¶: Get the number of bonds for which force field parameters have been defined.

int getNumPerBondParameters() const¶: Get the number of per-bond parameters that the interaction depends on.

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

const std::string &getEnergyFunction() const¶: Get the algebraic expression that gives the interaction energy for each bond

void setEnergyFunction(const std::string &energy)¶: Set the algebraic expression that gives the interaction energy for 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.

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 addBond(int particle1, int particle2, const std::vector<double> &parameters = std::vector< double >())¶

Add a bond term to the force field.

Parameters:

particle1 – the index of the first particle connected by the bond
particle2 – the index of the second particle connected by the bond
parameters – the list of parameters for the new bond

Returns:	the index of the bond that was added

void getBondParameters(int index, int &particle1, int &particle2, std::vector<double> &parameters) const¶

Get the force field parameters for a bond term.

Parameters:

index – the index of the bond for which to get parameters
particle1 – [out] the index of the first particle connected by the bond
particle2 – [out] the index of the second particle connected by the bond
parameters – [out] the list of parameters for the bond

void setBondParameters(int index, int particle1, int particle2, const std::vector<double> &parameters = std::vector< double >())¶

Set the force field parameters for a bond term.

Parameters:

index – the index of the bond for which to set parameters
particle1 – the index of the first particle connected by the bond
particle2 – the index of the second particle connected by the bond
parameters – the list of parameters for the bond

void updateParametersInContext(Context &context)¶

Update the per-bond 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 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. 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.

bool usesPeriodicBoundaryConditions() const¶

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

Returns:	false