CustomCompoundBondForce¶
-
class
OpenMM
::
CustomCompoundBondForce
¶ This class supports a wide variety of bonded interactions. It defines a “bond” as a single energy term that depends on the positions of a fixed set of particles. The number of particles involved in a bond, and how the energy depends on their positions, is configurable. It may depend on the positions of individual particles, the distances between pairs of particles, the angles formed by sets of three particles, and the dihedral angles formed by sets of four particles.
We refer to the particles in a bond as p1, p2, p3, etc. For each bond,
CustomCompoundBondForce
evaluates a user supplied algebraic expression to determine the interaction energy. The expression may depend on the following variables and functions:x1, y1, z1, x2, y2, z2, etc.: The x, y, and z coordinates of the particle positions. For example, x1 is the x coordinate of particle p1, and y3 is the y coordinate of particle p3.
distance(p1, p2): the distance between particles p1 and p2 (where “p1” and “p2” may be replaced by the names of whichever particles you want to calculate the distance between).
angle(p1, p2, p3): the angle formed by the three specified particles.
dihedral(p1, p2, p3, p4): the dihedral angle formed by the four specified particles, guaranteed to be in the range [-pi,+pi].
The expression also may involve tabulated functions, and may depend on arbitrary global and per-bond parameters.
To use this class, create a
CustomCompoundBondForce
object, passing an algebraic expression to the constructor that defines the interaction energy of each bond. 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()
.Next, call
addBond()
to define bonds and specify their parameter values. 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
CustomCompoundBondForce
that implements a Urey-Bradley potential. This is an interaction between three particles that depends on the angle formed by p1-p2-p3, and on the distance between p1 and p3.CustomCompoundBondForce* force = new CustomCompoundBondForce(3, "0.5*(kangle*(angle(p1,p2,p3)-theta0)^2+kbond*(distance(p1,p3)-r0)^2)");
This force depends on four parameters: kangle, kbond, theta0, and r0. The following code defines these as per-bond parameters:
force->addPerBondParameter("kangle"); force->addPerBondParameter("kbond"); force->addPerBondParameter("theta0"); 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.
In addition, you can call
addTabulatedFunction()
to define a new function based on tabulated values. You specify the function by creating aTabulatedFunction
object. That function can then appear in the expression.Methods
Create a
CustomCompoundBondForce
.Get the number of particles used to define each bond.
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 number of tabulated functions that have been defined.
Get the number of tabulated functions that have been defined.
Get the algebraic expression that gives the interaction energy of each bond
Set the algebraic expression that gives the interaction energy of 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 to the force
Get the properties of a bond.
Set the properties of a bond.
Add a tabulated function that may appear in the energy expression.
Get a const reference to a tabulated function that may appear in the energy expression.
Get a reference to a tabulated function that may appear in the energy expression.
Get the name of a tabulated function that may appear in the energy expression.
Add a tabulated function that may appear in the energy expression.
Get the parameters for a tabulated function that may appear in the energy expression.
Set the parameters for a tabulated function that may appear in the energy expression.
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.
-
CustomCompoundBondForce
(int numParticles, const std::string &energy)¶ Create a
CustomCompoundBondForce()
.- Parameters
numParticles – the number of particles used to define each bond
energy – an algebraic expression giving the interaction energy of each bond as a function of particle positions, inter-particle distances, angles, and dihedrals, and any global and per-bond parameters
-
~CustomCompoundBondForce
()¶
-
int
getNumParticlesPerBond
() const¶ Get the number of particles used to define each bond.
-
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.
-
int
getNumTabulatedFunctions
() const¶ Get the number of tabulated functions that have been defined.
-
int
getNumFunctions
() const¶ Get the number of tabulated functions that have been defined.
Deprecated
This method exists only for backward compatibility. Use
getNumTabulatedFunctions()
instead.
-
const std::string &
getEnergyFunction
() const¶ Get the algebraic expression that gives the interaction energy of each bond
-
void
setEnergyFunction
(const std::string &energy)¶ Set the algebraic expression that gives the interaction energy of 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
(const std::vector<int> &particles, const std::vector<double> ¶meters = std::vector<double>())¶ Add a bond to the force
- Parameters
particles – the indices of the particles the bond depends on
parameters – the list of per-bond parameter values for the new bond
- Returns
the index of the bond that was added
-
void
getBondParameters
(int index, std::vector<int> &particles, std::vector<double> ¶meters) const¶ Get the properties of a bond.
- Parameters
index – the index of the bond to get
particles – [out] the indices of the particles in the bond
parameters – [out] the list of per-bond parameter values for the bond
-
void
setBondParameters
(int index, const std::vector<int> &particles, const std::vector<double> ¶meters = std::vector<double>())¶ Set the properties of a bond.
- Parameters
index – the index of the bond to set
particles – the indices of the particles in the bond
parameters – the list of per-bond parameter values for the bond
-
int
addTabulatedFunction
(const std::string &name, TabulatedFunction *function)¶ Add a tabulated function that may appear in the energy expression.
- Parameters
name – the name of the function as it appears in expressions
function – a
TabulatedFunction
object defining the function. TheTabulatedFunction
should have been created on the heap with the “new” operator. TheForce
takes over ownership of it, and deletes it when theForce
itself is deleted.
- Returns
the index of the function that was added
-
const TabulatedFunction &
getTabulatedFunction
(int index) const¶ Get a const reference to a tabulated function that may appear in the energy expression.
- Parameters
index – the index of the function to get
- Returns
the
TabulatedFunction
object defining the function
-
TabulatedFunction &
getTabulatedFunction
(int index)¶ Get a reference to a tabulated function that may appear in the energy expression.
- Parameters
index – the index of the function to get
- Returns
the
TabulatedFunction
object defining the function
-
const std::string &
getTabulatedFunctionName
(int index) const¶ Get the name of a tabulated function that may appear in the energy expression.
- Parameters
index – the index of the function to get
- Returns
the name of the function as it appears in expressions
-
int
addFunction
(const std::string &name, const std::vector<double> &values, double min, double max)¶ Add a tabulated function that may appear in the energy expression.
Deprecated
This method exists only for backward compatibility. Use
addTabulatedFunction()
instead.
-
void
getFunctionParameters
(int index, std::string &name, std::vector<double> &values, double &min, double &max) const¶ Get the parameters for a tabulated function that may appear in the energy expression.
Deprecated
This method exists only for backward compatibility. Use getTabulatedFunctionParameters() instead. If the specified function is not a
Continuous1DFunction
, this throws an exception.
-
void
setFunctionParameters
(int index, const std::string &name, const std::vector<double> &values, double min, double max)¶ Set the parameters for a tabulated function that may appear in the energy expression.
Deprecated
This method exists only for backward compatibility. Use setTabulatedFunctionParameters() instead. If the specified function is not a
Continuous1DFunction
, this throws an exception.
-
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