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OpenMM
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OpenMM
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This class supports a wide variety of bonded interactions. More...
Inheritance diagram for CustomCompoundBondForce:Public Member Functions | |
| def | getNumParticlesPerBond |
| getNumParticlesPerBond(CustomCompoundBondForce self) -> int | |
| def | getNumBonds |
| getNumBonds(CustomCompoundBondForce self) -> int | |
| def | getNumPerBondParameters |
| getNumPerBondParameters(CustomCompoundBondForce self) -> int | |
| def | getNumGlobalParameters |
| getNumGlobalParameters(CustomCompoundBondForce self) -> int | |
| def | getNumFunctions |
| getNumFunctions(CustomCompoundBondForce self) -> int | |
| def | getEnergyFunction |
| getEnergyFunction(CustomCompoundBondForce self) -> std::string const & | |
| def | setEnergyFunction |
| setEnergyFunction(CustomCompoundBondForce self, std::string const & energy) | |
| def | addPerBondParameter |
| addPerBondParameter(CustomCompoundBondForce self, std::string const & name) -> int | |
| def | getPerBondParameterName |
| getPerBondParameterName(CustomCompoundBondForce self, int index) -> std::string const & | |
| def | setPerBondParameterName |
| setPerBondParameterName(CustomCompoundBondForce self, int index, std::string const & name) | |
| def | addGlobalParameter |
| addGlobalParameter(CustomCompoundBondForce self, std::string const & name, double defaultValue) -> int | |
| def | getGlobalParameterName |
| getGlobalParameterName(CustomCompoundBondForce self, int index) -> std::string const & | |
| def | setGlobalParameterName |
| setGlobalParameterName(CustomCompoundBondForce self, int index, std::string const & name) | |
| def | getGlobalParameterDefaultValue |
| getGlobalParameterDefaultValue(CustomCompoundBondForce self, int index) -> double | |
| def | setGlobalParameterDefaultValue |
| setGlobalParameterDefaultValue(CustomCompoundBondForce self, int index, double defaultValue) | |
| def | addBond |
| addBond(CustomCompoundBondForce self, vectori particles, vectord parameters) -> int | |
| def | getBondParameters |
| getBondParameters(CustomCompoundBondForce self, int index) | |
| def | setBondParameters |
| setBondParameters(CustomCompoundBondForce self, int index, vectori particles, vectord parameters) | |
| def | addFunction |
| addFunction(CustomCompoundBondForce self, std::string const & name, vectord values, double min, double max) -> int | |
| def | getFunctionParameters |
| getFunctionParameters(CustomCompoundBondForce self, int index) | |
| def | setFunctionParameters |
| setFunctionParameters(CustomCompoundBondForce self, int index, std::string const & name, vectord values, double min, double max) | |
| def | updateParametersInContext |
| updateParametersInContext(CustomCompoundBondForce self, Context context) | |
| def | __init__ |
| init(OpenMM::CustomCompoundBondForce self, int numParticles, std::string const & energy) -> CustomCompoundBondForce init(OpenMM::CustomCompoundBondForce self, CustomCompoundBondForce other) -> CustomCompoundBondForce | |
| def | __del__ |
| del(OpenMM::CustomCompoundBondForce self) | |
| Public Member Functions inherited from Force | |
| def | __init__ |
| def | __del__ |
| del(OpenMM::Force self) | |
| def | getForceGroup |
| getForceGroup(Force self) -> int | |
| def | setForceGroup |
| setForceGroup(Force self, int group) | |
| def | __copy__ |
| def | __deepcopy__ |
Public Attributes | |
| this | |
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.
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 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().
Next, call addBond() to define bonds and specify their parameter values. 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 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");
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, step, delta. 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.
In addition, you can call addFunction() to define a new function based on tabulated values. You specify a vector of values, and a natural spline is created from them. That function can then appear in the expression.
| def __init__ | ( | self, | |
| args | |||
| ) |
init(OpenMM::CustomCompoundBondForce self, int numParticles, std::string const & energy) -> CustomCompoundBondForce init(OpenMM::CustomCompoundBondForce self, CustomCompoundBondForce other) -> CustomCompoundBondForce
Create a CustomCompoundBondForce.
| 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 |
| def __del__ | ( | self | ) |
del(OpenMM::CustomCompoundBondForce self)
| def addBond | ( | self, | |
| args | |||
| ) |
addBond(CustomCompoundBondForce self, vectori particles, vectord parameters) -> int
Add a bond to the force
| particles | the indices of the particles the bond depends on |
| parameters | the list of per-bond parameter values for the new bond |
| def addFunction | ( | self, | |
| args | |||
| ) |
addFunction(CustomCompoundBondForce self, std::string const & name, vectord values, double min, double max) -> int
Add a tabulated function that may appear in the energy expression.
| name | the name of the function as it appears in expressions |
| values | the tabulated values of the function f(x) at uniformly spaced values of x between min and max. The function is assumed to be zero for x < min or x > max. |
| min | the value of the independent variable corresponding to the first element of values |
| max | the value of the independent variable corresponding to the last element of values |
| def addGlobalParameter | ( | self, | |
| args | |||
| ) |
addGlobalParameter(CustomCompoundBondForce self, std::string const & name, double defaultValue) -> int
Add a new global parameter that the interaction may depend on.
| name | the name of the parameter |
| defaultValue | the default value of the parameter |
| def addPerBondParameter | ( | self, | |
| args | |||
| ) |
addPerBondParameter(CustomCompoundBondForce self, std::string const & name) -> int
Add a new per-bond parameter that the interaction may depend on.
| name | the name of the parameter |
| def getBondParameters | ( | self, | |
| args | |||
| ) |
getBondParameters(CustomCompoundBondForce self, int index)
Get the properties of a bond.
| index | the index of the bond to get |
| particles | the indices of the particles in the bond |
| parameters | the list of per-bond parameter values for the bond |
| def getEnergyFunction | ( | self | ) |
getEnergyFunction(CustomCompoundBondForce self) -> std::string const &
Get the algebraic expression that gives the interaction energy of each bond
| def getFunctionParameters | ( | self, | |
| args | |||
| ) |
getFunctionParameters(CustomCompoundBondForce self, int index)
Get the parameters for a tabulated function that may appear in the energy expression.
| index | the index of the function for which to get parameters |
| name | the name of the function as it appears in expressions |
| values | the tabulated values of the function f(x) at uniformly spaced values of x between min and max. The function is assumed to be zero for x < min or x > max. |
| min | the value of the independent variable corresponding to the first element of values |
| max | the value of the independent variable corresponding to the last element of values |
| def getGlobalParameterDefaultValue | ( | self, | |
| args | |||
| ) |
getGlobalParameterDefaultValue(CustomCompoundBondForce self, int index) -> double
Get the default value of a global parameter.
| index | the index of the parameter for which to get the default value |
| def getGlobalParameterName | ( | self, | |
| args | |||
| ) |
getGlobalParameterName(CustomCompoundBondForce self, int index) -> std::string const &
Get the name of a global parameter.
| index | the index of the parameter for which to get the name |
| def getNumBonds | ( | self | ) |
getNumBonds(CustomCompoundBondForce self) -> int
Get the number of bonds for which force field parameters have been defined.
| def getNumFunctions | ( | self | ) |
getNumFunctions(CustomCompoundBondForce self) -> int
Get the number of tabulated functions that have been defined.
| def getNumGlobalParameters | ( | self | ) |
getNumGlobalParameters(CustomCompoundBondForce self) -> int
Get the number of global parameters that the interaction depends on.
| def getNumParticlesPerBond | ( | self | ) |
getNumParticlesPerBond(CustomCompoundBondForce self) -> int
Get the number of particles used to define each bond.
| def getNumPerBondParameters | ( | self | ) |
getNumPerBondParameters(CustomCompoundBondForce self) -> int
Get the number of per-bond parameters that the interaction depends on.
| def getPerBondParameterName | ( | self, | |
| args | |||
| ) |
getPerBondParameterName(CustomCompoundBondForce self, int index) -> std::string const &
Get the name of a per-bond parameter.
| index | the index of the parameter for which to get the name |
| def setBondParameters | ( | self, | |
| args | |||
| ) |
setBondParameters(CustomCompoundBondForce self, int index, vectori particles, vectord parameters)
Set the properties of a bond.
| index | the index of the bond group to set |
| particles | the indices of the particles in the bond |
| parameters | the list of per-bond parameter values for the bond |
| def setEnergyFunction | ( | self, | |
| args | |||
| ) |
setEnergyFunction(CustomCompoundBondForce self, std::string const & energy)
Set the algebraic expression that gives the interaction energy of each bond
| def setFunctionParameters | ( | self, | |
| args | |||
| ) |
setFunctionParameters(CustomCompoundBondForce self, int index, std::string const & name, vectord values, double min, double max)
Set the parameters for a tabulated function that may appear in algebraic expressions.
| index | the index of the function for which to set parameters |
| name | the name of the function as it appears in expressions |
| values | the tabulated values of the function f(x) at uniformly spaced values of x between min and max. The function is assumed to be zero for x < min or x > max. |
| min | the value of the independent variable corresponding to the first element of values |
| max | the value of the independent variable corresponding to the last element of values |
| def setGlobalParameterDefaultValue | ( | self, | |
| args | |||
| ) |
setGlobalParameterDefaultValue(CustomCompoundBondForce self, int index, double defaultValue)
Set the default value of a global parameter.
| index | the index of the parameter for which to set the default value |
| name | the default value of the parameter |
| def setGlobalParameterName | ( | self, | |
| args | |||
| ) |
setGlobalParameterName(CustomCompoundBondForce self, int index, std::string const & name)
Set the name of a global parameter.
| index | the index of the parameter for which to set the name |
| name | the name of the parameter |
| def setPerBondParameterName | ( | self, | |
| args | |||
| ) |
setPerBondParameterName(CustomCompoundBondForce self, int index, std::string const & name)
Set the name of a per-bond parameter.
| index | the index of the parameter for which to set the name |
| name | the name of the parameter |
| def updateParametersInContext | ( | self, | |
| args | |||
| ) |
updateParametersInContext(CustomCompoundBondForce self, Context 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 updateParametersInState() 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.
| this |
1.8.2