CustomHbondForce¶
-
class
OpenMM
::
CustomHbondForce
¶ This class supports a wide variety of energy functions used to represent hydrogen bonding. It computes interactions between “donor” particle groups and “acceptor” particle groups, where each group may include up to three particles. Typically a donor group consists of a hydrogen atom and the atoms it is bonded to, and an acceptor group consists of a negatively charged atom and the atoms it is bonded to.
We refer to the particles in a donor group as d1, d2 and d3, and the particles in an acceptor group as a1, a2, and a3. For each donor and each acceptor,
CustomHbondForce
evaluates a user supplied algebraic expression to determine the interaction energy. The expression may depend on arbitrary distances, angles, and dihedral angles defined by any of the six particles involved. The function distance(p1, p2) is the distance between the particles p1 and p2 (where “p1” and “p2” should be replaced by the names of the actual particles to calculate the distance between), angle(p1, p2, p3) is the angle formed by the three specified particles, and dihedral(p1, p2, p3, p4) is the dihedral angle formed by the four specified particles.The expression also may involve tabulated functions, and may depend on arbitrary global, per-donor, and per-acceptor parameters. It also optionally supports periodic boundary conditions and cutoffs for long range interactions.
To use this class, create a
CustomHbondForce
object, passing an algebraic expression to the constructor that defines the interaction energy between each donor and acceptor. Then calladdPerDonorParameter()
to define per-donor parameters,addPerAcceptorParameter()
to define per-acceptor parameters, andaddGlobalParameter()
to define global parameters. The values of per-donor and per-acceptor 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
addDonor()
andaddAcceptor()
to define donors and acceptors and specify their parameter values. After a donor or acceptor has been added, you can modify its parameters by callingsetDonorParameters()
orsetAcceptorParameters()
. This will have no effect on Contexts that already exist unless you callupdateParametersInContext()
.CustomHbondForce
also lets you specify “exclusions”, particular combinations of donors and acceptors whose interactions should be omitted from force and energy calculations. This is most often used for particles that are bonded to each other.As an example, the following code creates a
CustomHbondForce
that implements a simple harmonic potential to keep the distance between a1 and d1, and the angle formed by a1-d1-d2, near ideal values:CustomHbondForce* force = new CustomHbondForce("k*(distance(a1,d1)-r0)^2*(angle(a1,d1,d2)-theta0)^2");
This force depends on three parameters: k, r0, and theta0. The following code defines these as per-donor parameters:
force->addPerDonorParameter("k"); force->addPerDonorParameter("r0"); force->addPerDonorParameter("theta0");
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
CustomHbondForce
.Get the number of donors for which force field parameters have been defined.
Get the number of acceptors for which force field parameters have been defined.
Get the number of donor-acceptor pairs whose interactions should be excluded.
Get the number of per-donor parameters that the interaction depends on.
Get the number of per-acceptor parameters that the interaction depends on.
Get the number of global parameters that the interaction depends on.
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 between a donor and an acceptor
Set the algebraic expression that gives the interaction energy between a donor and an acceptor
Get the method used for handling long range nonbonded interactions.
Set the method used for handling long range nonbonded interactions.
Get the cutoff distance (in nm) being used.
Set the cutoff distance (in nm) being used.
Add a new per-donor parameter that the interaction may depend on.
Get the name of a per-donor parameter.
Set the name of a per-donor parameter.
Add a new per-acceptor parameter that the interaction may depend on.
Get the name of a per-acceptor parameter.
Set the name of a per-acceptor 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.
Add a donor group to the force
Get the properties of a donor group.
Set the properties of a donor group.
Add an acceptor group to the force
Get the properties of an acceptor group.
Set the properties of an acceptor group.
Add a donor-acceptor pair to the list of interactions that should be excluded.
Get the donor and acceptor in a pair whose interaction should be excluded.
Get the donor and acceptor in a pair whose interaction should be excluded.
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-donor and per-acceptor parameters in a
Context
to match those stored in thisForce
object.Returns whether or not this force makes use of periodic boundary conditions.
Enum: NonbondedMethod
NoCutoff
No cutoff is applied to nonbonded interactions. The full set of N^2 interactions is computed exactly. This necessarily means that periodic boundary conditions cannot be used. This is the default.
CutoffNonPeriodic
Interactions beyond the cutoff distance are ignored.
CutoffPeriodic
Periodic boundary conditions are used, so that each particle interacts only with the nearest periodic copy of each other particle. Interactions beyond the cutoff distance are ignored.
-
CustomHbondForce
(const std::string &energy)¶ Create a
CustomHbondForce()
.- Parameters
energy – an algebraic expression giving the interaction energy between a donor and an acceptor as a function of inter-particle distances, angles, and dihedrals, as well as any global, per-donor, and per-acceptor parameters
-
~CustomHbondForce
()¶
-
int
getNumDonors
() const¶ Get the number of donors for which force field parameters have been defined.
-
int
getNumAcceptors
() const¶ Get the number of acceptors for which force field parameters have been defined.
-
int
getNumExclusions
() const¶ Get the number of donor-acceptor pairs whose interactions should be excluded.
-
int
getNumPerDonorParameters
() const¶ Get the number of per-donor parameters that the interaction depends on.
-
int
getNumPerAcceptorParameters
() const¶ Get the number of per-acceptor 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 between a donor and an acceptor
-
void
setEnergyFunction
(const std::string &energy)¶ Set the algebraic expression that gives the interaction energy between a donor and an acceptor
-
NonbondedMethod
getNonbondedMethod
() const¶ Get the method used for handling long range nonbonded interactions.
-
void
setNonbondedMethod
(NonbondedMethod method)¶ Set the method used for handling long range nonbonded interactions.
-
double
getCutoffDistance
() const¶ Get the cutoff distance (in nm) being used. All interactions for which the distance between d1 and a1 is greater than the cutoff will be ignored. If the NonbondedMethod in use is NoCutoff, this value will have no effect.
- Returns
the cutoff distance, measured in nm
-
void
setCutoffDistance
(double distance)¶ Set the cutoff distance (in nm) being used. All interactions for which the distance between d1 and a1 is greater than the cutoff will be ignored. If the NonbondedMethod in use is NoCutoff, this value will have no effect.
- Parameters
distance – the cutoff distance, measured in nm
-
int
addPerDonorParameter
(const std::string &name)¶ Add a new per-donor 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 &
getPerDonorParameterName
(int index) const¶ Get the name of a per-donor parameter.
- Parameters
index – the index of the parameter for which to get the name
- Returns
the parameter name
-
void
setPerDonorParameterName
(int index, const std::string &name)¶ Set the name of a per-donor parameter.
- Parameters
index – the index of the parameter for which to set the name
name – the name of the parameter
-
int
addPerAcceptorParameter
(const std::string &name)¶ Add a new per-acceptor 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 &
getPerAcceptorParameterName
(int index) const¶ Get the name of a per-acceptor parameter.
- Parameters
index – the index of the parameter for which to get the name
- Returns
the parameter name
-
void
setPerAcceptorParameterName
(int index, const std::string &name)¶ Set the name of a per-acceptor 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
-
int
addDonor
(int d1, int d2, int d3, const std::vector<double> ¶meters = std::vector<double>())¶ Add a donor group to the force
- Parameters
d1 – the index of the first particle for this donor group
d2 – the index of the second particle for this donor group. If the group only includes one particle, this must be -1.
d3 – the index of the third particle for this donor group. If the group includes less than three particles, this must be -1.
parameters – the list of per-donor parameter values for the new donor
- Returns
the index of the donor that was added
-
void
getDonorParameters
(int index, int &d1, int &d2, int &d3, std::vector<double> ¶meters) const¶ Get the properties of a donor group.
- Parameters
index – the index of the donor group to get
d1 – [out] the index of the first particle for this donor group
d2 – [out] the index of the second particle for this donor group. If the group only includes one particle, this will be -1.
d3 – [out] the index of the third particle for this donor group. If the group includes less than three particles, this will be -1.
parameters – [out] the list of per-donor parameter values for the donor
-
void
setDonorParameters
(int index, int d1, int d2, int d3, const std::vector<double> ¶meters = std::vector<double>())¶ Set the properties of a donor group.
- Parameters
index – the index of the donor group to set
d1 – the index of the first particle for this donor group
d2 – the index of the second particle for this donor group. If the group only includes one particle, this must be -1.
d3 – the index of the third particle for this donor group. If the group includes less than three particles, this must be -1.
parameters – the list of per-donor parameter values for the donor
-
int
addAcceptor
(int a1, int a2, int a3, const std::vector<double> ¶meters = std::vector<double>())¶ Add an acceptor group to the force
- Parameters
a1 – the index of the first particle for this acceptor group
a2 – the index of the second particle for this acceptor group. If the group only includes one particle, this must be -1.
a3 – the index of the third particle for this acceptor group. If the group includes less than three particles, this must be -1.
parameters – the list of per-acceptor parameter values for the new acceptor
- Returns
the index of the acceptor that was added
-
void
getAcceptorParameters
(int index, int &a1, int &a2, int &a3, std::vector<double> ¶meters) const¶ Get the properties of an acceptor group.
- Parameters
index – the index of the acceptor group to get
a1 – [out] the index of the first particle for this acceptor group
a2 – [out] the index of the second particle for this acceptor group. If the group only includes one particle, this will be -1.
a3 – [out] the index of the third particle for this acceptor group. If the group includes less than three particles, this will be -1.
parameters – [out] the list of per-acceptor parameter values for the acceptor
-
void
setAcceptorParameters
(int index, int a1, int a2, int a3, const std::vector<double> ¶meters = std::vector<double>())¶ Set the properties of an acceptor group.
- Parameters
index – the index of the acceptor group to set
a1 – the index of the first particle for this acceptor group
a2 – the index of the second particle for this acceptor group. If the group only includes one particle, this must be -1.
a3 – the index of the third particle for this acceptor group. If the group includes less than three particles, this must be -1.
parameters – the list of per-acceptor parameter values for the acceptor
-
int
addExclusion
(int donor, int acceptor)¶ Add a donor-acceptor pair to the list of interactions that should be excluded.
- Parameters
donor – the index of the donor to exclude
acceptor – the index of the acceptor to exclude
- Returns
the index of the exclusion that was added
-
void
getExclusionParticles
(int index, int &donor, int &acceptor) const¶ Get the donor and acceptor in a pair whose interaction should be excluded.
- Parameters
index – the index of the exclusion for which to get donor and acceptor indices
donor – [out] the index of the donor
acceptor – [out] the index of the acceptor
-
void
setExclusionParticles
(int index, int donor, int acceptor)¶ Get the donor and acceptor in a pair whose interaction should be excluded.
- Parameters
index – the index of the exclusion for which to get donor and acceptor indices
donor – the index of the donor
acceptor – the index of the acceptor
-
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-donor and per-acceptor 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 callsetDonorParameters()
andsetAcceptorParameters()
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-donor and per-acceptor parameters. All other aspects of the
Force
(the energy function, nonbonded method, cutoff distance, etc.) are unaffected and can only be changed by reinitializing theContext
. The set of particles involved in a donor or acceptor cannot be changed, nor can new donors or acceptors be added.
-
bool
usesPeriodicBoundaryConditions
() const¶ Returns whether or not this force makes use of periodic boundary conditions.
- Returns
true if force uses PBC and false otherwise
-