CustomBondForce

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

This class implements bonded interactions between pairs of particles. Unlike HarmonicBondForce, the functional form of the interaction is completely customizable, and may involve arbitrary algebraic expressions. It may depend on the distance between particles, as well as on arbitrary global and per-bond parameters.

To use this class, create a CustomBondForce object, passing an algebraic expression to the constructor that defines the interaction energy between each pair of bonded particles. The expression may depend on r, the distance between the particles, as well as on any parameters you choose. Then call addPerBondParameter() to define per-bond parameters, and addGlobalParameter() to define global parameters. The values of per-bond 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 addBond() once for each bond. After a bond has been added, you can modify its parameters by calling setBondParameters(). This will have no effect on Contexts that already exist unless you call updateParametersInContext().

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

CustomBondForce* force = new CustomBondForce("0.5*k*(r-r0)^2");

This force depends on two parameters: the spring constant k and equilibrium distance r0. The following code defines these parameters:

force->addPerBondParameter("k");
force->addPerBondParameter("r0");

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) → CustomBondForce

__init__(self, other) -> CustomBondForce

Create a CustomBondForce.

Parameters:energy (string) – an algebraic expression giving the interaction energy between two bonded particles as a function of r, the distance between them

Methods

__init__((self, energy) -> CustomBondForce) __init__(self, other) -> CustomBondForce
addBond((self, particle1, particle2, ...) addBond(self, particle1, particle2) -> int
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.
addPerBondParameter((self, name) -> int) Add a new per-bond parameter that the interaction may depend on.
getBondParameters(self, index) Get the force field parameters for a bond term.
getEnergyFunction((self) -> std::string const &) Get the algebraic expression that gives the interaction energy for each bond
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.
getNumBonds((self) -> int) Get the number of bonds for which force field parameters have been defined.
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.
getNumPerBondParameters((self) -> int) Get the number of per-bond parameters that the interaction depends on.
getPerBondParameterName((self, ...) Get the name of a per-bond parameter.
setBondParameters(self, index, particle1, ...) setBondParameters(self, index, particle1, particle2)
setEnergyFunction(self, energy) Set the algebraic expression that gives the interaction energy for each bond
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.
setPerBondParameterName(self, index, name) Set the name of a per-bond parameter.
setUsesPeriodicBoundaryConditions(self, periodic) Set whether this force should apply periodic boundary conditions when calculating displacements.
updateParametersInContext(self, context) Update the per-bond 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.
getNumBonds(self) → int

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

getNumPerBondParameters(self) → int

Get the number of per-bond 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 bond

setEnergyFunction(self, energy)

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

addPerBondParameter(self, name) → int

Add a new per-bond 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
getPerBondParameterName(self, index) → std::string const &

Get the name of a per-bond parameter.

Parameters:index (int) – the index of the parameter for which to get the name
Returns:the parameter name
Return type:string
setPerBondParameterName(self, index, name)

Set the name of a per-bond 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
addBond(self, particle1, particle2, parameters) → int

addBond(self, particle1, particle2) -> int

Add a bond term to the force field.

Parameters:
  • particle1 (int) – the index of the first particle connected by the bond
  • particle2 (int) – the index of the second particle connected by the bond
  • parameters (vector< double >) – the list of parameters for the new bond
Returns:

the index of the bond that was added

Return type:

int

getBondParameters(self, index)

Get the force field parameters for a bond term.

Parameters:index (int) – the index of the bond for which to get parameters
Returns:
  • particle1 (int) – the index of the first particle connected by the bond
  • particle2 (int) – the index of the second particle connected by the bond
  • parameters (vector< double >) – the list of parameters for the bond
setBondParameters(self, index, particle1, particle2, parameters)

setBondParameters(self, index, particle1, particle2)

Set the force field parameters for a bond term.

Parameters:
  • index (int) – the index of the bond for which to set parameters
  • particle1 (int) – the index of the first particle connected by the bond
  • particle2 (int) – the index of the second particle connected by the bond
  • parameters (vector< double >) – the list of parameters for the bond
updateParametersInContext(self, context)

Update the per-bond 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 setBondParameters() 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-bond 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 bond cannot be changed, nor can new bonds 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).