CustomTorsionForce¶

class OpenMM::CustomTorsionForce¶

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.

Methods

`CustomTorsionForce()`	Create a `CustomTorsionForce()`.
`getNumTorsions()`	Get the number of torsions for which force field parameters have been defined.
`getNumPerTorsionParameters()`	Get the number of per-torsion 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 torsion
`setEnergyFunction()`	Set the algebraic expression that gives the interaction energy for each torsion
`addPerTorsionParameter()`	Add a new per-torsion parameter that the interaction may depend on.
`getPerTorsionParameterName()`	Get the name of a per-torsion parameter.
`setPerTorsionParameterName()`	Set the name of a per-torsion 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.
`addTorsion()`	Add a torsion term to the force field.
`getTorsionParameters()`	Get the force field parameters for a torsion term.
`setTorsionParameters()`	Set the force field parameters for a torsion term.
`updateParametersInContext()`	Update the per-torsion 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.

CustomTorsionForce(const std::string &energy)¶

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

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

int getNumPerTorsionParameters() const¶: Get the number of per-torsion 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 torsion

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

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

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 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

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

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

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 – [out] the index of the first particle connected by the torsion
particle2 – [out] the index of the second particle connected by the torsion
particle3 – [out] the index of the third particle connected by the torsion
particle4 – [out] the index of the fourth particle connected by the torsion
parameters – [out] the list of parameters for the torsion

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

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¶

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

Returns:	true if force uses PBC and false otherwise