OpenMM
CustomTorsionForce Class Reference

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

+ Inheritance diagram for CustomTorsionForce:

List of all members.

Public Member Functions

def getNumTorsions
 getNumTorsions(self) -> int
def getNumPerTorsionParameters
 getNumPerTorsionParameters(self) -> int
def getNumGlobalParameters
 getNumGlobalParameters(self) -> int
def getEnergyFunction
 getEnergyFunction(self) -> std::string const &
def setEnergyFunction
 Set the algebraic expression that gives the interaction energy for each torsion.
def addPerTorsionParameter
 addPerTorsionParameter(self, name) -> int
def getPerTorsionParameterName
 getPerTorsionParameterName(self, index) -> std::string const &
def setPerTorsionParameterName
 Set the name of a per-torsion parameter.
def addGlobalParameter
 addGlobalParameter(self, name, defaultValue) -> int
def getGlobalParameterName
 getGlobalParameterName(self, index) -> std::string const &
def setGlobalParameterName
 Set the name of a global parameter.
def getGlobalParameterDefaultValue
 getGlobalParameterDefaultValue(self, index) -> double
def setGlobalParameterDefaultValue
 Set the default value of a global parameter.
def addTorsion
 addTorsion(self, particle1, particle2, particle3, particle4, parameters) -> int addTorsion(self, particle1, particle2, particle3, particle4) -> int
def getTorsionParameters
 Get the force field parameters for a torsion term.
def setTorsionParameters
 Set the force field parameters for a torsion term.
def updateParametersInContext
 Update the per-torsion parameters in a Context to match those stored in this Force object.
def usesPeriodicBoundaryConditions
 usesPeriodicBoundaryConditions(self) -> bool
def __init__
 __init__(self, energy) -> CustomTorsionForce __init__(self, other) -> CustomTorsionForce

Public Attributes

 this

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

def __init__ (   self,
  args 
)

__init__(self, energy) -> CustomTorsionForce __init__(self, other) -> CustomTorsionForce

Create a CustomTorsionForce.

Parameters:
energy(string) an algebraic expression giving the interaction energy between three particles as a function of theta, the torsion angle between them

Member Function Documentation

def addGlobalParameter (   self,
  name,
  defaultValue 
)

addGlobalParameter(self, name, defaultValue) -> int

Add a new global parameter that the interaction may depend on.

Parameters:
name(string) the name of the parameter
defaultValue(double) the default value of the parameter
Returns:
(int) the index of the parameter that was added
def addPerTorsionParameter (   self,
  name 
)

addPerTorsionParameter(self, name) -> int

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

Parameters:
name(string) the name of the parameter
Returns:
(int) the index of the parameter that was added
def addTorsion (   self,
  args 
)

addTorsion(self, particle1, particle2, particle3, particle4, parameters) -> int addTorsion(self, particle1, particle2, particle3, particle4) -> int

Add a torsion term to the force field.

Parameters:
particle1(int) the index of the first particle connected by the torsion
particle2(int) the index of the second particle connected by the torsion
particle3(int) the index of the third particle connected by the torsion
particle4(int) the index of the fourth particle connected by the torsion
parameters(vector< double >) the list of parameters for the new torsion
Returns:
(int) the index of the torsion that was added
def getEnergyFunction (   self)

getEnergyFunction(self) -> std::string const &

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

def getGlobalParameterDefaultValue (   self,
  index 
)

getGlobalParameterDefaultValue(self, index) -> double

Get the default value of a global parameter.

Parameters:
index(int) the index of the parameter for which to get the default value
Returns:
(double) the parameter default value
def getGlobalParameterName (   self,
  index 
)

getGlobalParameterName(self, index) -> std::string const &

Get the name of a global parameter.

Parameters:
index(int) the index of the parameter for which to get the name
Returns:
(string) the parameter name
def getNumGlobalParameters (   self)

getNumGlobalParameters(self) -> int

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

getNumPerTorsionParameters(self) -> int

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

def getNumTorsions (   self)

getNumTorsions(self) -> int

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

def getPerTorsionParameterName (   self,
  index 
)

getPerTorsionParameterName(self, index) -> std::string const &

Get the name of a per-torsion parameter.

Parameters:
index(int) the index of the parameter for which to get the name
Returns:
(string) the parameter name
def getTorsionParameters (   self,
  index 
)

Get the force field parameters for a torsion term.

Parameters:
index(int) the index of the torsion for which to get parameters
Returns:
(int) the index of the first particle connected by the torsion
(int) the index of the second particle connected by the torsion
(int) the index of the third particle connected by the torsion
(int) the index of the fourth particle connected by the torsion
(vector< double >) the list of parameters for the torsion
def setEnergyFunction (   self,
  energy 
)

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

def setGlobalParameterDefaultValue (   self,
  index,
  defaultValue 
)

Set the default value of a global parameter.

Parameters:
index(int) the index of the parameter for which to set the default value
defaultValue(double) the default value of the parameter
def setGlobalParameterName (   self,
  index,
  name 
)

Set the name of a global parameter.

Parameters:
index(int) the index of the parameter for which to set the name
name(string) the name of the parameter
def setPerTorsionParameterName (   self,
  index,
  name 
)

Set the name of a per-torsion parameter.

Parameters:
index(int) the index of the parameter for which to set the name
name(string) the name of the parameter
def setTorsionParameters (   self,
  args 
)

Set the force field parameters for a torsion term.

Parameters:
index(int) the index of the torsion for which to set parameters
particle1(int) the index of the first particle connected by the torsion
particle2(int) the index of the second particle connected by the torsion
particle3(int) the index of the third particle connected by the torsion
particle4(int) the index of the fourth particle connected by the torsion
parameters(vector< double >) the list of parameters for the torsion
def updateParametersInContext (   self,
  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.

usesPeriodicBoundaryConditions(self) -> bool

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

Returns:
(bool) true if force uses PBC and false otherwise

Reimplemented from Force.


Member Data Documentation

Reimplemented from Force.


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