CustomManyParticleForce¶

class
OpenMM::
CustomManyParticleForce
¶ This class supports a wide variety of nonbonded Nparticle interactions, where N is user specified. The interaction energy is determined by an arbitrary, user specified algebraic expression that is evaluated for every possible set of N particles in the system. It may depend on the positions of the 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.
Be aware that the cost of evaluating an Nparticle interaction increases very rapidly with N. Values larger than N=3 are rarely used.
We refer to a set of particles for which the energy is being evaluated as p1, p2, p3, etc. The energy 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.
 arbitrary global and perparticle parameters that you define.
To use this class, create a
CustomManyParticleForce()
object, passing an algebraic expression to the constructor that defines the interaction energy of each set of particles. Then calladdPerParticleParameter()
to define perparticle parameters, andaddGlobalParameter()
to define global parameters. The values of perparticle 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 perparticle 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()
.Multiparticle interactions can be very expensive to evaluate, so they are usually used with a cutoff distance. The exact interpretation of the cutoff depends on the permutation mode, as discussed below.
CustomManyParticleForce()
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. If you specify a pair of particles as an exclusion,As an example, the following code creates a
CustomManyParticleForce()
that implements an AxilrodTeller potential. This is an interaction between three particles that depends on all three distances and angles formed by the particles.CustomManyParticleForce* force = new CustomManyParticleForce(3, "C*(1+3*cos(theta1)*cos(theta2)*cos(theta3))/(r12*r13*r23)^3;" "theta1=angle(p1,p2,p3); theta2=angle(p2,p3,p1); theta3=angle(p3,p1,p2);" "r12=distance(p1,p2); r13=distance(p1,p3); r23=distance(p2,p3)"); force>setPermutationMode(CustomManyParticleForce::SinglePermutation);
This force depends on one parameter, C. The following code defines it as a global parameter:
force>addGlobalParameter("C", 1.0);
Notice that the expression is symmetric with respect to the particles. It only depends on the products cos(theta1)*cos(theta2)*cos(theta3) and r12*r13*r23, both of which are unchanged if the labels p1, p2, and p3 are permuted. This is required because we specified SinglePermutation as the permutation mode. (This is the default, so we did not really need to set it, but doing so makes the example clearer.) In this mode, the expression is only evaluated once for each set of particles. No guarantee is made about which particle will be identified as p1, p2, etc. Therefore, the energy
Not all manyparticle interactions work this way. Another common pattern is for the expression to describe an interaction between one central particle and other nearby particles. An example of this is the 3particle piece of the StillingerWeber potential:
CustomManyParticleForce* force = new CustomManyParticleForce(3, "L*eps*(cos(theta1)+1/3)^2*exp(sigma*gamma/(r12a*sigma))*exp(sigma*gamma/(r13a*sigma));" "r12 = distance(p1,p2); r13 = distance(p1,p3); theta1 = angle(p3,p1,p2)"); force>setPermutationMode(CustomManyParticleForce::UniqueCentralParticle);
When the permutation mode is set to UniqueCentralParticle, particle p1 is treated as the central particle. For a set of N particles, the expression is evaluated N times, once with each particle as p1. The expression can therefore treat p1 differently from the other particles. Notice that it is still symmetric with respect to p2 and p3, however. There is no guarantee about how those labels will be assigned to particles.
Distance cutoffs are applied in different ways depending on the permutation mode. In SinglePermutation mode, every particle in the set must be within the cutoff distance of every other particle. If
Another common situation is that some particles are fundamentally different from others, causing the expression to be inherently nonsymmetric. An example would be a water model that involves three particles, two of which
A particle type is an integer that you specify when you call
addParticle()
. (If you omit the argument, it defaults to 0.) For the water model, you could specify 0 for all oxygen atoms and 1 for all hydrogen atoms. You can then callsetTypeFilter()
to specify the list of allowed types for each of the N particles involved in an interaction:set<int> oxygenTypes, hydrogenTypes; oxygenTypes.insert(0); hydrogenTypes.insert(1); force>setTypeFilter(0, oxygenTypes); force>setTypeFilter(1, hydrogenTypes); force>setTypeFilter(2, hydrogenTypes);
This specifies that of the three particles in an interaction, p1 must be oxygen while p2 and p3 must be hydrogen. The energy expression will only be evaluated for triplets of particles that satisfy those requirements. It will still only be evaluated once for each triplet, so it must still be symmetric with respect to p2 and p3.
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. The names of perparticle parameters have the suffix “1”, “2”, etc. appended to them to indicate the values for the multiple interacting particles. For example, if you define a perparticle parameter called “charge”, then the variable “charge2” is the charge of particle p2. As seen above, 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
CustomManyParticleForce()
Create a CustomManyParticleForce()
.~CustomManyParticleForce()
getNumParticlesPerSet()
Get the number of particles in each set for which the energy is evaluated getNumParticles()
Get the number of particles for which force field parameters have been defined. getNumExclusions()
Get the number of particle pairs whose interactions should be excluded. getNumPerParticleParameters()
Get the number of perparticle 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. 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 getNonbondedMethod()
Get the method used for handling long range nonbonded interactions. setNonbondedMethod()
Set the method used for handling long range nonbonded interactions. getPermutationMode()
Get the mode that selects which permutations of a set of particles to evaluate the interaction for. setPermutationMode()
Set the mode that selects which permutations of a set of particles to evaluate the interaction for. getCutoffDistance()
Get the cutoff distance (in nm) being used for nonbonded interactions. setCutoffDistance()
Set the cutoff distance (in nm) being used for nonbonded interactions. addPerParticleParameter()
Add a new perparticle parameter that the interaction may depend on. getPerParticleParameterName()
Get the name of a perparticle parameter. setPerParticleParameterName()
Set the name of a perparticle 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. addParticle()
Add the nonbonded force parameters for a particle. getParticleParameters()
Get the nonbonded force parameters for a particle. setParticleParameters()
Set the nonbonded force parameters for a particle. addExclusion()
Add a particle pair to the list of interactions that should be excluded. getExclusionParticles()
Get the particles in a pair whose interaction should be excluded. setExclusionParticles()
Set the particles in a pair whose interaction should be excluded. createExclusionsFromBonds()
Identify exclusions based on the molecular topology. getTypeFilter()
Get the allowed particle types for one of the particles involved in the interaction. setTypeFilter()
Set the allowed particle types for one of the particles involved in the interaction. 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 perparticle parameters in a Context
to match those stored in thisForce
object.usesPeriodicBoundaryConditions()
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 interactions is computed exactly. This necessarily means that periodic boundary conditions cannot be used. This is the default. CutoffNonPeriodic Interactions are ignored if any two particles are further apart than the cutoff distance. CutoffPeriodic Periodic boundary conditions are used, so that each particle interacts only with the nearest periodic copy of each other particle. Interactions are ignored if any two particles are further apart than the cutoff distance. Enum: PermutationMode
SinglePermutation For any set of particles, the interaction is evaluated only once for a single permutation of the particles. There is no guarantee about which permutation will be used (aside from the requirement to satisfy type filters), so the expression must be symmetric. If cutoffs are used, then every particle in the set must be within the cutoff distance of every other particle. UniqueCentralParticle The interaction is treated as an interaction between one central particle (p1) and various other nearby particles (p2, p3, ...). For a set of N particles it will be evaluated N times, once with each particle as p1. The expression must be symmetric with respect to the other particles, but may treat p1 differently. If cutoffs are used, then every particle must be within the cutoff distance of p1. 
CustomManyParticleForce
(int particlesPerSet, const std::string &energy)¶ Create a
CustomManyParticleForce()
.Parameters:  particlesPerSet – the number of particles in each set for which the energy is evaluated
 energy – an algebraic expression giving the interaction energy of each triplet as a function of particle positions, interparticle distances, angles, and any global and perparticle parameters

~CustomManyParticleForce
()¶

int
getNumParticlesPerSet
() const¶ Get the number of particles in each set for which the energy is evaluated

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 perparticle 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.

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

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.

PermutationMode
getPermutationMode
() const¶ Get the mode that selects which permutations of a set of particles to evaluate the interaction for.

void
setPermutationMode
(PermutationMode mode)¶ Set the mode that selects which permutations of a set of particles to evaluate the interaction for.

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

int
addPerParticleParameter
(const std::string &name)¶ Add a new perparticle 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 perparticle 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 perparticle 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

int
addParticle
(const std::vector<double> ¶meters = std::vector< double >(), int type = 0)¶ 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
 type – the type of the new particle
Returns: the index of the particle that was added

void
getParticleParameters
(int index, std::vector<double> ¶meters, int &type) 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
 type – [out] the type of the specified particle

void
setParticleParameters
(int index, const std::vector<double> ¶meters, int type)¶ 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
 type – the type of 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

void
getTypeFilter
(int index, std::set<int> &types) const¶ Get the allowed particle types for one of the particles involved in the interaction. If this an empty set (the default), no filter is applied and all interactions are evaluated regardless of the type of the specified particle.
Parameters:  index – the index of the particle within the interaction (between 0 and
getNumParticlesPerSet()
)  types – [out] the allowed types for the specified particle
 index – the index of the particle within the interaction (between 0 and

void
setTypeFilter
(int index, const std::set<int> &types)¶ Set the allowed particle types for one of the particles involved in the interaction. If this an empty set (the default), no filter is applied and all interactions are evaluated regardless of the type of the specified particle.
Parameters:  index – the index of the particle within the interaction (between 0 and
getNumParticlesPerSet()
)  types – the allowed types for the specified particle
 index – the index of the particle within the interaction (between 0 and

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 perparticle 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 perparticle 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