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);
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
CustomCentroidBondForce
.Get the number of groups used to define each bond.
Get the number of particle groups that have been defined.
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 particle group.
Get the properties of a group.
Set the properties of a group.
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.
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.
-
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
()¶
-
int
getNumGroupsPerBond
() const¶ Get the number of groups used to define each bond.
-
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
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
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.
-
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
-
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
-
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.
-
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