CustomNonbondedForce¶
-
class
OpenMM
::
CustomNonbondedForce
¶ This class implements nonbonded interactions between particles. Unlike
NonbondedForce
, the functional form of the interaction is completely customizable, and may involve arbitrary algebraic expressions and tabulated functions. It may depend on the distance between particles, as well as on arbitrary global and per-particle parameters. It also optionally supports periodic boundary conditions and cutoffs for long range interactions.To use this class, create a
CustomNonbondedForce
object, passing an algebraic expression to the constructor that defines the interaction energy between each pair of particles. The expression may depend on r, the distance between the particles, as well as on any parameters you choose. Then calladdPerParticleParameter()
to define per-particle parameters, andaddGlobalParameter()
to define global parameters. The values of per-particle 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
addParticle()
once for each particle in theSystem
to set the values of its per-particle parameters. The number of particles for which you set parameters must be exactly equal to the number of particles in theSystem
, or else an exception will be thrown when you try to create aContext
. After a particle has been added, you can modify its parameters by callingsetParticleParameters()
. This will have no effect on Contexts that already exist unless you callupdateParametersInContext()
.CustomNonbondedForce
also lets you specify “exclusions”, particular pairs of particles 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
CustomNonbondedForce
that implements a 12-6 Lennard-Jones potential:CustomNonbondedForce* force = new CustomNonbondedForce("4*epsilon*((sigma/r)^12-(sigma/r)^6); sigma=0.5*(sigma1+sigma2); epsilon=sqrt(epsilon1*epsilon2)");
This force depends on two parameters: sigma and epsilon. The following code defines these as per-particle parameters:
force->addPerParticleParameter("sigma"); force->addPerParticleParameter("epsilon");
The expression
CustomNonbondedForce
can operate in two modes. By default, it computes the interaction of every particle in theSystem
with every other particle. Alternatively, you can restrict it to only a subset of particle pairs. To do this, specify one or more “interaction groups”. An interaction group consists of two sets of particles that should interact with each other. Every particle in the first set interacts with every particle in the second set. For example, you might use this feature to compute a solute-solvent interaction energy, while omitting all interactions between two solute atoms or two solvent atoms.To create an interaction group, call
addInteractionGroup()
. You may add as many interaction groups as you want. Be aware of the following:Exclusions are still taken into account, so the interactions between excluded pairs are omitted.
Likewise, a particle will never interact with itself, even if it appears in both sets of an interaction group.
If a particle pair appears in two different interaction groups, its interaction will be computed twice. This is sometimes useful, but be aware of it so you do not accidentally create unwanted duplicate interactions.
If you do not add any interaction groups to a
CustomNonbondedForce
, it operates in the default mode where every particle interacts with every other particle.
When using a cutoff, by default the interaction is sharply truncated at the cutoff distance. Optionally you can instead use a switching function to make the interaction smoothly go to zero over a finite distance range. To enable this, call
setUseSwitchingFunction()
. You must also callsetSwitchingDistance()
to specify the distance at which the interaction should begin to decrease. The switching distance must be less than the cutoff distance. Of course, you could also incorporate the switching function directly into your energy expression, but there are several advantages to keeping it separate. It makes your energy expression simpler to write and understand. It allows you to use the same energy expression with or without a cutoff. Also, when using a long range correction (see below), separating out the switching function allows the correction to be calculated more accurately.Another optional feature of this class is to add a contribution to the energy which approximates the effect of all interactions beyond the cutoff in a periodic system. When running a simulation at constant pressure, this can improve the quality of the result. Call
setUseLongRangeCorrection()
to enable it.Computing the long range correction takes negligible work in each time step, but it does require an expensive precomputation at the start of the simulation. Furthermore, that precomputation must be repeated every time a global parameter changes (or when you modify per-particle parameters by calling
updateParametersInContext()
). This means that if parameters change frequently, the long range correction can be very slow. For this reason, it is disabled by default.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. The names of per-particle parameters have the suffix “1” or “2” appended to them to indicate the values for the two interacting particles. As seen in the above example, the expression may also involve intermediate quantities that are defined following the main expression, using “;” as a separator.
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
CustomNonbondedForce
.Get the number of particles for which force field parameters have been defined.
Get the number of particle pairs whose interactions should be excluded.
Get the number of per-particle 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 number of interaction groups that have been defined.
Get the number of global parameters with respect to which the derivative of the energy should be computed.
Get the algebraic expression that gives the interaction energy between two particles
Set the algebraic expression that gives the interaction energy between two particles
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 for nonbonded interactions.
Set the cutoff distance (in nm) being used for nonbonded interactions.
Get whether a switching function is applied to the interaction.
Set whether a switching function is applied to the interaction.
Get the distance at which the switching function begins to reduce the interaction.
Set the distance at which the switching function begins to reduce the interaction.
Get whether to add a correction to the energy to compensate for the cutoff and switching function.
Set whether to add a correction to the energy to compensate for the cutoff and switching function.
Add a new per-particle parameter that the interaction may depend on.
Get the name of a per-particle parameter.
Set the name of a per-particle 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 the nonbonded force parameters for a particle.
Get the nonbonded force parameters for a particle.
Set the nonbonded force parameters for a particle.
Add a particle pair to the list of interactions that should be excluded.
Get the particles in a pair whose interaction should be excluded.
Set the particles in a pair whose interaction should be excluded.
Identify exclusions based on the molecular topology.
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.
Add an interaction group.
Get the parameters for an interaction group.
Set the parameters for an interaction group.
Update the per-particle 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.
-
CustomNonbondedForce
(const std::string &energy)¶ Create a
CustomNonbondedForce()
.- Parameters
energy – an algebraic expression giving the interaction energy between two particles as a function of r, the distance between them, as well as any global and per-particle parameters
-
CustomNonbondedForce
(const CustomNonbondedForce &rhs)¶
-
~CustomNonbondedForce
()¶
-
int
getNumParticles
() const¶ Get the number of particles for which force field parameters have been defined.
-
int
getNumExclusions
() const¶ Get the number of particle pairs whose interactions should be excluded.
-
int
getNumPerParticleParameters
() const¶ Get the number of per-particle 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.
-
int
getNumInteractionGroups
() const¶ Get the number of interaction groups that have been defined.
-
int
getNumEnergyParameterDerivatives
() const¶ Get the number of global parameters with respect to which the derivative of the energy should be computed.
-
const std::string &
getEnergyFunction
() const¶ Get the algebraic expression that gives the interaction energy between two particles
-
void
setEnergyFunction
(const std::string &energy)¶ Set the algebraic expression that gives the interaction energy between two particles
-
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 for nonbonded interactions. 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 for nonbonded interactions. If the NonbondedMethod in use is NoCutoff, this value will have no effect.
- Parameters
distance – the cutoff distance, measured in nm
-
bool
getUseSwitchingFunction
() const¶ Get whether a switching function is applied to the interaction. If the nonbonded method is set to NoCutoff, this option is ignored.
-
void
setUseSwitchingFunction
(bool use)¶ Set whether a switching function is applied to the interaction. If the nonbonded method is set to NoCutoff, this option is ignored.
-
double
getSwitchingDistance
() const¶ Get the distance at which the switching function begins to reduce the interaction. This must be less than the cutoff distance.
-
void
setSwitchingDistance
(double distance)¶ Set the distance at which the switching function begins to reduce the interaction. This must be less than the cutoff distance.
-
bool
getUseLongRangeCorrection
() const¶ Get whether to add a correction to the energy to compensate for the cutoff and switching function. This has no effect if periodic boundary conditions are not used.
-
void
setUseLongRangeCorrection
(bool use)¶ Set whether to add a correction to the energy to compensate for the cutoff and switching function. This has no effect if periodic boundary conditions are not used.
-
int
addPerParticleParameter
(const std::string &name)¶ Add a new per-particle 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 &
getPerParticleParameterName
(int index) const¶ Get the name of a per-particle parameter.
- Parameters
index – the index of the parameter for which to get the name
- Returns
the parameter name
-
void
setPerParticleParameterName
(int index, const std::string &name)¶ Set the name of a per-particle 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
addParticle
(const std::vector<double> ¶meters = std::vector<double>())¶ Add the nonbonded force parameters for a particle. This should be called once for each particle in the
System
. When it is called for the i’th time, it specifies the parameters for the i’th particle.- Parameters
parameters – the list of parameters for the new particle
- Returns
the index of the particle that was added
-
void
getParticleParameters
(int index, std::vector<double> ¶meters) const¶ Get the nonbonded force parameters for a particle.
- Parameters
index – the index of the particle for which to get parameters
parameters – [out] the list of parameters for the specified particle
-
void
setParticleParameters
(int index, const std::vector<double> ¶meters)¶ Set the nonbonded force parameters for a particle.
- Parameters
index – the index of the particle for which to set parameters
parameters – the list of parameters for the specified particle
-
int
addExclusion
(int particle1, int particle2)¶ Add a particle pair to the list of interactions that should be excluded.
In many cases, you can use
createExclusionsFromBonds()
rather than adding each exclusion explicitly.- Parameters
particle1 – the index of the first particle in the pair
particle2 – the index of the second particle in the pair
- Returns
the index of the exclusion that was added
-
void
getExclusionParticles
(int index, int &particle1, int &particle2) const¶ Get the particles in a pair whose interaction should be excluded.
- Parameters
index – the index of the exclusion for which to get particle indices
particle1 – [out] the index of the first particle in the pair
particle2 – [out] the index of the second particle in the pair
-
void
setExclusionParticles
(int index, int particle1, int particle2)¶ Set the particles in a pair whose interaction should be excluded.
- Parameters
index – the index of the exclusion for which to set particle indices
particle1 – the index of the first particle in the pair
particle2 – the index of the second particle in the pair
-
void
createExclusionsFromBonds
(const std::vector<std::pair<int, int>> &bonds, int bondCutoff)¶ Identify exclusions based on the molecular topology. Particles which are separated by up to a specified number of bonds are added as exclusions.
- Parameters
bonds – the set of bonds based on which to construct exclusions. Each element specifies the indices of two particles that are bonded to each other.
bondCutoff – pairs of particles that are separated by this many bonds or fewer are added to the list of exclusions
-
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.
-
int
addInteractionGroup
(const std::set<int> &set1, const std::set<int> &set2)¶ Add an interaction group. An interaction will be computed between every particle in set1 and every particle in set2.
- Parameters
set1 – the first set of particles forming the interaction group
set2 – the second set of particles forming the interaction group
- Returns
the index of the interaction group that was added
-
void
getInteractionGroupParameters
(int index, std::set<int> &set1, std::set<int> &set2) const¶ Get the parameters for an interaction group.
- Parameters
index – the index of the interaction group for which to get parameters
set1 – [out] the first set of particles forming the interaction group
set2 – [out] the second set of particles forming the interaction group
-
void
setInteractionGroupParameters
(int index, const std::set<int> &set1, const std::set<int> &set2)¶ Set the parameters for an interaction group.
- Parameters
index – the index of the interaction group for which to set parameters
set1 – the first set of particles forming the interaction group
set2 – the second set of particles forming the interaction group
-
void
updateParametersInContext
(Context &context)¶ Update the per-particle 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 callsetParticleParameters()
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-particle 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
. Also, this method cannot be used to add new particles, only to change the parameters of existing ones.
-
bool
usesPeriodicBoundaryConditions
() const¶ Returns whether or not this force makes use of periodic boundary conditions.
- Returns
true if force uses PBC and false otherwise