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(). Note that theta is guaranteed to be in the range [-pi,+pi], which may cause issues with force discontinuities if the energy function does not respect this domain.

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

CustomTorsionForce* force = new CustomTorsionForce("0.5*k*(1-cos(theta-theta0))");

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");

If a harmonic restraint is desired, it is important to be careful of the domain for theta, using an idiom like this:

CustomTorsionForce* force = new CustomTorsionForce("0.5*k*min(dtheta, 2*pi-dtheta)^2; dtheta = abs(theta-theta0); pi = 3.1415926535");

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, 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.
getNumEnergyParameterDerivatives Get the number of global parameters with respect to which the derivative of the energy should be computed.
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.
addEnergyParameterDerivative Request that this Force compute the derivative of its energy with respect to a global parameter.
getEnergyParameterDerivativeName Get the name of a global parameter with respect to which this Force should compute the derivative of the energy.
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.
setUsesPeriodicBoundaryConditions Set whether this force should apply periodic boundary conditions when calculating displacements.
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.

int getNumEnergyParameterDerivatives() const

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

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. 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:
Returns:the parameter name
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.

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.

bool usesPeriodicBoundaryConditions() const

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

Returns:true if force uses PBC and false otherwise