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CustomTorsionForce Class Reference

This class implements interactions between sets of four particles that depend on the torsion angle between them. More...

`#include <CustomTorsionForce.h>`

Inheritance diagram for CustomTorsionForce:

## Public Member Functions

| CustomTorsionForce (const std::string &energy)
| Create a CustomTorsionForce. More...
int | getNumTorsions () const
| Get the number of torsions for which force field parameters have been defined. More...
int | getNumPerTorsionParameters () const
| Get the number of per-torsion parameters that the interaction depends on. More...
int | getNumGlobalParameters () const
| Get the number of global parameters that the interaction depends on. More...
const std::string & | getEnergyFunction () const
| Get the algebraic expression that gives the interaction energy for each torsion. More...
void | setEnergyFunction (const std::string &energy)
| Set the algebraic expression that gives the interaction energy for each torsion. More...
int | addPerTorsionParameter (const std::string &name)
| Add a new per-torsion parameter that the interaction may depend on. More...
const std::string & | getPerTorsionParameterName (int index) const
| Get the name of a per-torsion parameter. More...
void | setPerTorsionParameterName (int index, const std::string &name)
| Set the name of a per-torsion parameter. More...
int | addGlobalParameter (const std::string &name, double defaultValue)
| Add a new global parameter that the interaction may depend on. More...
const std::string & | getGlobalParameterName (int index) const
| Get the name of a global parameter. More...
void | setGlobalParameterName (int index, const std::string &name)
| Set the name of a global parameter. More...
double | getGlobalParameterDefaultValue (int index) const
| Get the default value of a global parameter. More...
void | setGlobalParameterDefaultValue (int index, double defaultValue)
| Set the default value of a global parameter. More...
int | addTorsion (int particle1, int particle2, int particle3, int particle4, const std::vector< double > &parameters)
| Add a torsion term to the force field. More...
void | getTorsionParameters (int index, int &particle1, int &particle2, int &particle3, int &particle4, std::vector< double > &parameters) const
| Get the force field parameters for a torsion term. More...
void | setTorsionParameters (int index, int particle1, int particle2, int particle3, int particle4, const std::vector< double > &parameters)
| Set the force field parameters for a torsion term. More...
void | updateParametersInContext (Context &context)
| Update the per-torsion parameters in a Context to match those stored in this Force object. More...
bool | usesPeriodicBoundaryConditions () const
| Returns whether or not this force makes use of periodic boundary conditions. More...
Public Member Functions inherited from Force
| Force ()
virtual | ~Force ()
int | getForceGroup () const
| Get the force group this Force belongs to. More...
void | setForceGroup (int group)
| Set the force group this Force belongs to. More...

## Protected Member Functions

ForceImpl * | createImpl () const
| When a Context is created, it invokes this method on each Force in the System. More...
Protected Member Functions inherited from Force
ForceImpl & | getImplInContext (Context &context)
| Get the ForceImpl corresponding to this Force in a Context. More...
ContextImpl & | getContextImpl (Context &context)
| Get the ContextImpl corresponding to a Context. More...

## Detailed Description

This class implements interactions between sets of four particles that depend on the torsion angle between them.

Unlike PeriodicTorsionForce, the functional form of the interaction is completely customizable, and may involve arbitrary algebraic expressions. In addition to the angle formed by the particles, it may depend on arbitrary global and per-torsion parameters.

To use this class, create a CustomTorsionForce object, passing an algebraic expression to the constructor that defines the interaction energy between each set of particles. The expression may depend on theta, the torsion angle formed by the particles, as well as on any parameters you choose. Then call addPerTorsionParameter() to define per-torsion parameters, and addGlobalParameter() to define global parameters. The values of per-torsion 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 addTorsion() once for each torsion. After an torsion has been added, you can modify its parameters by calling setTorsionParameters(). This will have no effect on Contexts that already exist unless you call updateParametersInContext().

As an example, the following code creates a CustomTorsionForce that implements a harmonic potential:

`CustomTorsionForce* force = new CustomTorsionForce("0.5*k*(theta-theta0)^2");`

This force depends on two parameters: the spring constant k and equilibrium angle theta0. The following code defines these parameters:

``

    force->addPerTorsionParameter("k");
    force->addPerTorsionParameter("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.

## Constructor & Destructor Documentation

CustomTorsionForce | ( | const std::string & | energy | ) |

explicit

Create a CustomTorsionForce.

Parameters

  energy | an algebraic expression giving the interaction energy between three particles as a function of theta, the torsion angle between them

## Member Function Documentation

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

int addPerTorsionParameter | ( | const std::string & | name | ) |

Add a new per-torsion parameter that the interaction may depend on.

Parameters

  name | the name of the parameter

Returns
  the index of the parameter that was added

int addTorsion | ( | int | particle1,
|  | int | particle2,
|  | int | particle3,
|  | int | particle4,
|  | const std::vector< double > & | parameters
| ) |  |

Add a torsion term to the force field.

Parameters

  particle1 | the index of the first particle connected by the torsion
  particle2 | the index of the second particle connected by the torsion
  particle3 | the index of the third particle connected by the torsion
  particle4 | the index of the fourth particle connected by the torsion
  parameters | the list of parameters for the new torsion

Returns
  the index of the torsion that was added

ForceImpl* createImpl | ( |  | ) | const

protectedvirtual

When a Context is created, it invokes this method on each Force in the System.

It should create a new ForceImpl object which can be used by the context for calculating forces. The ForceImpl will be deleted automatically when the Context is deleted.

Implements Force.

const std::string& getEnergyFunction | ( |  | ) | const

Get the algebraic expression that gives the interaction energy for each torsion.

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

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

int getNumGlobalParameters | ( |  | ) | const

inline

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

int getNumPerTorsionParameters | ( |  | ) | const

inline

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

int getNumTorsions | ( |  | ) | const

inline

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

const std::string& getPerTorsionParameterName | ( | int | index | ) | const

Get the name of a per-torsion parameter.

Parameters

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

Returns
  the parameter name

void getTorsionParameters | ( | int | index,
|  | int & | particle1,
|  | int & | particle2,
|  | int & | particle3,
|  | int & | particle4,
|  | std::vector< double > & | parameters
| ) |  | const

Get the force field parameters for a torsion term.

Parameters

  index | the index of the torsion for which to get parameters
  particle1 | the index of the first particle connected by the torsion
  particle2 | the index of the second particle connected by the torsion
  particle3 | the index of the third particle connected by the torsion
  particle4 | the index of the fourth particle connected by the torsion
  parameters | the list of parameters for the torsion

void setEnergyFunction | ( | const std::string & | energy | ) |

Set the algebraic expression that gives the interaction energy for each torsion.

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
  name | the default value of the parameter

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

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

Set the name of a per-torsion parameter.

Parameters

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

void setTorsionParameters | ( | int | index,
|  | int | particle1,
|  | int | particle2,
|  | int | particle3,
|  | int | particle4,
|  | const std::vector< double > & | parameters
| ) |  |

Set the force field parameters for a torsion term.

Parameters

  index | the index of the torsion for which to set parameters
  particle1 | the index of the first particle connected by the torsion
  particle2 | the index of the second particle connected by the torsion
  particle3 | the index of the third particle connected by the torsion
  particle4 | the index of the fourth particle connected by the torsion
  parameters | the list of parameters for the torsion

void updateParametersInContext | ( | Context & | context | ) |

Update the per-torsion 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 setTorsionParameters() 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-torsion 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 torsion cannot be changed, nor can new torsions be added.

bool usesPeriodicBoundaryConditions | ( |  | ) | const

inlinevirtual

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

Returns
  true if force uses PBC and false otherwise

Reimplemented from Force.

The documentation for this class was generated from the following file:

- CustomTorsionForce.h