CustomCentroidBondForce¶
-
class
OpenMM::
CustomCentroidBondForce
¶ This class is similar to
CustomCompoundBondForce
, but instead of applying forces between individual particles, it applies them between the centers of groups of particles. This is useful for a variety of purposes, such as restraints to keep two molecules from moving too far apart.When using this class, you define groups of particles, and the center of each group is calculated as a weighted average of the particle positions. By default, the particle masses are used as weights, so the center position is the center of mass. You can optionally specify different weights to use. You then add bonds just as with
CustomCompoundBondForce
, but instead of specifying the particles that make up a bond, you specify the groups.When creating a
CustomCentroidBondForce()
, you specify the number of groups involved in a bond, and an expression for the energy of each bond. It may depend on the center positions of individual groups, the distances between the centers of pairs of groups, the angles formed by sets of three groups, and the dihedral angles formed by sets of four groups.We refer to the groups in a bond as g1, g2, g3, etc. For each bond,
CustomCentroidBondForce()
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 centers of the groups. For example, x1 is the x coordinate of the center of group g1, and y3 is the y coordinate of the center of group g3.
- distance(g1, g2): the distance between the centers of groups g1 and g2 (where “g1” and “g2” may be replaced by the names of whichever groups you want to calculate the distance between).
- angle(g1, g2, g3): the angle formed by the centers of the three specified groups.
- dihedral(g1, g2, g3, g4): the dihedral angle formed by the centers of the four specified groups.
The expression also may involve tabulated functions, and may depend on arbitrary global and per-bond parameters.
To use this class, create a
CustomCentroidBondForce()
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
addGroup()
to define the particle groups. Each group is specified by the particles it contains, and the weights to use when computing the center position.Then 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
CustomCentroidBondForce()
that implements a harmonic force between the centers of mass of two groups of particles.CustomCentroidBondForce* force = new CustomCentroidBondForce(2, "0.5*k*distance(g1,g2)^2"); force->addPerBondParameter("k"); force->addGroup(particles1); force->addGroup(particles2); vector<int> bondGroups; bondGroups.push_back(0); bondGroups.push_back(1); vector<double> bondParameters; bondParameters.push_back(k); force->addBond(bondGroups, bondParameters);
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.
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
CustomCentroidBondForce()
Create a CustomCentroidBondForce()
.~CustomCentroidBondForce()
getNumGroupsPerBond()
Get the number of groups used to define each bond. getNumGroups()
Get the number of particle groups that have been defined. getNumBonds()
Get the number of bonds for which force field parameters have been defined. getNumPerBondParameters()
Get the number of per-bond parameters that the interaction depends on. getNumGlobalParameters()
Get the number of global parameters that the interaction depends on. getNumTabulatedFunctions()
Get the number of tabulated functions that have been defined. getNumFunctions()
Get the number of tabulated functions that have been defined. getEnergyFunction()
Get the algebraic expression that gives the interaction energy of each bond setEnergyFunction()
Set the algebraic expression that gives the interaction energy of each bond addPerBondParameter()
Add a new per-bond parameter that the interaction may depend on. getPerBondParameterName()
Get the name of a per-bond parameter. setPerBondParameterName()
Set the name of a per-bond parameter. addGlobalParameter()
Add a new global parameter that the interaction may depend on. getGlobalParameterName()
Get the name of a global parameter. setGlobalParameterName()
Set the name of a global parameter. getGlobalParameterDefaultValue()
Get the default value of a global parameter. setGlobalParameterDefaultValue()
Set the default value of a global parameter. addGroup()
Add a particle group. getGroupParameters()
Get the properties of a group. setGroupParameters()
Set the properties of a group. addBond()
Add a bond to the force getBondParameters()
Get the properties of a bond. setBondParameters()
Set the properties of a bond. addTabulatedFunction()
Add a tabulated function that may appear in the energy expression. getTabulatedFunction()
Get a const reference to a tabulated function that may appear in the energy expression. getTabulatedFunction()
Get a reference to a tabulated function that may appear in the energy expression. getTabulatedFunctionName()
Get the name of a tabulated function that may appear in the energy expression. updateParametersInContext()
Update the per-bond parameters in a Context
to match those stored in thisForce
object.usesPeriodicBoundaryConditions()
Returns whether or not this force makes use of periodic boundary conditions. -
CustomCentroidBondForce
(int numGroups, const std::string &energy)¶ Create a
CustomCentroidBondForce()
.Parameters: - numGroups – the number of groups 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
-
~CustomCentroidBondForce
()¶
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int
getNumGroupsPerBond
() const¶ Get the number of groups used to define each bond.
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int
getNumGroups
() const¶ Get the number of particle groups that have been defined.
-
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
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.
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
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int
addGroup
(const std::vector<int> &particles, const std::vector<double> &weights = std::vector< double >())¶ Add a particle group.
Parameters: - particles – the indices of the particles to include in the group
- weights – the weight to use for each particle when computing the center position. If this is omitted, then particle masses will be used as weights.
Returns: the index of the group that was added
-
void
getGroupParameters
(int index, std::vector<int> &particles, std::vector<double> &weights) const¶ Get the properties of a group.
Parameters: - index – the index of the group to get
- particles – [out] the indices of the particles in the group
- weights – [out] the weight used for each particle when computing the center position. If no weights were specified, this vector will be empty indicating that particle masses should be used as weights.
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void
setGroupParameters
(int index, const std::vector<int> &particles, const std::vector<double> &weights = std::vector< double >())¶ Set the properties of a group.
Parameters: - index – the index of the group to set
- particles – the indices of the particles in the group
- weights – the weight to use for each particle when computing the center position. If this is omitted, then particle masses will be used as weights.
-
int
addBond
(const std::vector<int> &groups, const std::vector<double> ¶meters = std::vector< double >())¶ Add a bond to the force
Parameters: - groups – the indices of the groups 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
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void
getBondParameters
(int index, std::vector<int> &groups, std::vector<double> ¶meters) const¶ Get the properties of a bond.
Parameters: - index – the index of the bond to get
- groups – [out] the indices of the groups in the bond
- parameters – [out] the list of per-bond parameter values for the bond
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void
setBondParameters
(int index, const std::vector<int> &groups, const std::vector<double> ¶meters = std::vector< double >())¶ Set the properties of a bond.
Parameters: - index – the index of the bond to set
- groups – the indices of the groups 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
-
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
. Neither the definitions of groups nor the set of groups involved in a bond can be changed, nor can new bonds be added.
-
bool
usesPeriodicBoundaryConditions
() const¶ Returns whether or not this force makes use of periodic boundary conditions.
Returns: false