CustomTorsionForce

class simtk.openmm.openmm.CustomTorsionForce(*args)

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.

__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

Methods

__init__((self, energy) -> CustomTorsionForce) __init__(self, other) -> CustomTorsionForce
addEnergyParameterDerivative(self, name) Request that this Force compute the derivative of its energy with respect to a global parameter.
addGlobalParameter((self, name, ...) Add a new global parameter that the interaction may depend on.
addPerTorsionParameter((self, name) -> int) Add a new per-torsion parameter that the interaction may depend on.
addTorsion((self, particle1, particle2, ...) addTorsion(self, particle1, particle2, particle3, particle4) -> int
getEnergyFunction((self) -> std::string const &) Get the algebraic expression that gives the interaction energy for each torsion
getEnergyParameterDerivativeName((self, ...) Get the name of a global parameter with respect to which this Force should compute the derivative of the energy.
getForceGroup((self) -> int) Get the force group this Force belongs to.
getGlobalParameterDefaultValue((self, ...) Get the default value of a global parameter.
getGlobalParameterName((self, ...) Get the name of a global parameter.
getNumEnergyParameterDerivatives((self) -> int) Get the number of global parameters with respect to which the derivative of the energy should be computed.
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.
getNumTorsions((self) -> int) Get the number of torsions for which force field parameters have been defined.
getPerTorsionParameterName((self, ...) Get the name of a per-torsion parameter.
getTorsionParameters(self, index) Get the force field parameters for a torsion term.
setEnergyFunction(self, energy) Set the algebraic expression that gives the interaction energy for each torsion
setForceGroup(self, group) Set the force group this Force belongs to.
setGlobalParameterDefaultValue(self, index, ...) Set the default value of a global parameter.
setGlobalParameterName(self, index, name) Set the name of a global parameter.
setPerTorsionParameterName(self, index, name) Set the name of a per-torsion parameter.
setTorsionParameters(self, index, particle1, ...) setTorsionParameters(self, index, particle1, particle2, particle3, particle4)
setUsesPeriodicBoundaryConditions(self, periodic) Set whether this force should apply periodic boundary conditions when calculating displacements.
updateParametersInContext(self, context) Update the per-torsion parameters in a Context to match those stored in this Force object.
usesPeriodicBoundaryConditions((self) -> bool) Returns whether or not this force makes use of periodic boundary conditions.
getNumTorsions(self) → int

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

getNumPerTorsionParameters(self) → int

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

getNumGlobalParameters(self) → int

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

getNumEnergyParameterDerivatives(self) → int

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

getEnergyFunction(self) → std::string const &

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

setEnergyFunction(self, energy)

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

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:the index of the parameter that was added
Return type:int
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:the parameter name
Return type:string
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
addGlobalParameter(self, name, defaultValue) → int

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 (string) – the name of the parameter
  • defaultValue (double) – the default value of the parameter
Returns:

the index of the parameter that was added

Return type:

int

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:the parameter name
Return type:string
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
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:the parameter default value
Return type:double
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
addEnergyParameterDerivative(self, 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 (string) – the name of the parameter
getEnergyParameterDerivativeName(self, index) → std::string const &

Get the name of a global parameter with respect to which this Force should compute the derivative of the energy.

Parameters:index (int) – the index of the parameter derivative, between 0 and getNumEnergyParameterDerivatives()
Returns:the parameter name
Return type:string
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:

the index of the torsion that was added

Return type:

int

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:
  • 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
setTorsionParameters(self, index, particle1, particle2, particle3, particle4, parameters)

setTorsionParameters(self, index, particle1, particle2, particle3, particle4)

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
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.

setUsesPeriodicBoundaryConditions(self, 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.

usesPeriodicBoundaryConditions(self) → bool

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

Returns:true if force uses PBC and false otherwise
Return type:bool
__delattr__

x.__delattr__(‘name’) <==> del x.name

__format__()

default object formatter

__getattribute__

x.__getattribute__(‘name’) <==> x.name

__hash__
__reduce__()

helper for pickle

__reduce_ex__()

helper for pickle

__sizeof__() → int

size of object in memory, in bytes

__str__
getForceGroup(self) → int

Get the force group this Force belongs to.

setForceGroup(self, group)

Set the force group this Force belongs to.

Parameters:group (int) – the group index. Legal values are between 0 and 31 (inclusive).