CustomBondForce¶
-
class
OpenMM
::
CustomBondForce
¶ 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 calladdPerBondParameter()
to define per-bond parameters, andaddGlobalParameter()
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 callingContext::setParameter()
. Finally, calladdBond()
once for each bond. After a bond has been added, you can modify its parameters by callingsetBondParameters()
. This will have no effect on Contexts that already exist unless you callupdateParametersInContext()
.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 aContext
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, atan2, 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
Create a
CustomBondForce
.Get the number of bonds for which force field parameters have been defined.
Get the number of per-bond parameters that the interaction depends on.
Get the number of global parameters that the interaction depends on.
Get the number of global parameters with respect to which the derivative of the energy should be computed.
Get the algebraic expression that gives the interaction energy for each bond
Set the algebraic expression that gives the interaction energy for each bond
Add a new per-bond parameter that the interaction may depend on.
Get the name of a per-bond parameter.
Set the name of a per-bond parameter.
Add a new global parameter that the interaction may depend on.
Get the name of a global parameter.
Set the name of a global parameter.
Get the default value of a global parameter.
Set the default value of a global parameter.
Request that this
Force
compute the derivative of its energy with respect to a global parameter.Get the name of a global parameter with respect to which this
Force
should compute the derivative of the energy.Add a bond term to the force field.
Get the force field parameters for a bond term.
Set the force field parameters for a bond term.
Update the per-bond parameters in a
Context
to match those stored in thisForce
object.Set whether this force should apply periodic boundary conditions when calculating displacements.
Returns whether or not this force makes use of periodic boundary conditions.
-
CustomBondForce
(const std::string &energy)¶ Create a
CustomBondForce()
.- Parameters
energy – an algebraic expression giving the interaction energy between two bonded particles as a function of r, the distance between them
-
int
getNumBonds
() const¶ Get the number of bonds for which force field parameters have been defined.
-
int
getNumPerBondParameters
() const¶ Get the number of per-bond 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 bond
-
void
setEnergyFunction
(const std::string &energy)¶ Set the algebraic expression that gives the interaction energy for each bond
-
int
addPerBondParameter
(const std::string &name)¶ Add a new per-bond 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 &
getPerBondParameterName
(int index) const¶ Get the name of a per-bond parameter.
- Parameters
index – the index of the parameter for which to get the name
- Returns
the parameter name
-
void
setPerBondParameterName
(int index, const std::string &name)¶ Set the name of a per-bond 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 withaddGlobalParameter()
.- 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
index – the index of the parameter derivative, between 0 and
getNumEnergyParameterDerivatives()
- Returns
the parameter name
-
int
addBond
(int particle1, int particle2, const std::vector<double> ¶meters = std::vector<double>())¶ Add a bond term to the force field.
- Parameters
particle1 – the index of the first particle connected by the bond
particle2 – the index of the second particle connected by the bond
parameters – the list of parameters for the new bond
- Returns
the index of the bond that was added
-
void
getBondParameters
(int index, int &particle1, int &particle2, std::vector<double> ¶meters) const¶ Get the force field parameters for a bond term.
- Parameters
index – the index of the bond for which to get parameters
particle1 – [out] the index of the first particle connected by the bond
particle2 – [out] the index of the second particle connected by the bond
parameters – [out] the list of parameters for the bond
-
void
setBondParameters
(int index, int particle1, int particle2, const std::vector<double> ¶meters = std::vector<double>())¶ Set the force field parameters for a bond term.
- Parameters
index – the index of the bond for which to set parameters
particle1 – the index of the first particle connected by the bond
particle2 – the index of the second particle connected by the bond
parameters – the list of parameters for the bond
-
void
updateParametersInContext
(Context &context)¶ Update the per-bond parameters in a
Context
to match those stored in thisForce
object. This method provides an efficient method to update certain parameters in an existingContext
without needing to reinitialize it. Simply callsetBondParameters()
to modify this object’s parameters, then callupdateParametersInContext()
to copy them over to theContext
.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 theContext
. The set of particles involved in a bond cannot be changed, nor can new bonds 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
-