OpenMM

This class supports a wide variety of nonbonded Nparticle interactions, where N is user specified. More...
Public Member Functions  
def  getNumParticlesPerSet 
getNumParticlesPerSet(self) > int  
def  getNumParticles 
getNumParticles(self) > int  
def  getNumExclusions 
getNumExclusions(self) > int  
def  getNumPerParticleParameters 
getNumPerParticleParameters(self) > int  
def  getNumGlobalParameters 
getNumGlobalParameters(self) > int  
def  getNumTabulatedFunctions 
getNumTabulatedFunctions(self) > int  
def  getEnergyFunction 
getEnergyFunction(self) > std::string const &  
def  setEnergyFunction 
Set the algebraic expression that gives the interaction energy of each bond.  
def  getNonbondedMethod 
getNonbondedMethod(self) > OpenMM::CustomManyParticleForce::NonbondedMethod  
def  setNonbondedMethod 
Set the method used for handling long range nonbonded interactions.  
def  getPermutationMode 
getPermutationMode(self) > OpenMM::CustomManyParticleForce::PermutationMode  
def  setPermutationMode 
Set the mode that selects which permutations of a set of particles to evaluate the interaction for.  
def  getCutoffDistance 
getCutoffDistance(self) > double  
def  setCutoffDistance 
Set the cutoff distance (in nm) being used for nonbonded interactions.  
def  addPerParticleParameter 
addPerParticleParameter(self, name) > int  
def  getPerParticleParameterName 
getPerParticleParameterName(self, index) > std::string const &  
def  setPerParticleParameterName 
Set the name of a perparticle parameter.  
def  addGlobalParameter 
addGlobalParameter(self, name, defaultValue) > int  
def  getGlobalParameterName 
getGlobalParameterName(self, index) > std::string const &  
def  setGlobalParameterName 
Set the name of a global parameter.  
def  getGlobalParameterDefaultValue 
getGlobalParameterDefaultValue(self, index) > double  
def  setGlobalParameterDefaultValue 
Set the default value of a global parameter.  
def  addParticle 
addParticle(self, parameters, type=0) > int addParticle(self, parameters) > int addParticle(self) > int  
def  getParticleParameters 
Get the nonbonded force parameters for a particle.  
def  setParticleParameters 
Set the nonbonded force parameters for a particle.  
def  addExclusion 
addExclusion(self, particle1, particle2) > int  
def  getExclusionParticles 
Get the particles in a pair whose interaction should be excluded.  
def  setExclusionParticles 
Set the particles in a pair whose interaction should be excluded.  
def  createExclusionsFromBonds 
Identify exclusions based on the molecular topology.  
def  getTypeFilter 
Get the allowed particle types for one of the particles involved in the interaction.  
def  setTypeFilter 
Set the allowed particle types for one of the particles involved in the interaction.  
def  addTabulatedFunction 
addTabulatedFunction(self, name, function) > int  
def  getTabulatedFunction 
getTabulatedFunction(self, index) > TabulatedFunction getTabulatedFunction(self, index) > TabulatedFunction  
def  getTabulatedFunctionName 
getTabulatedFunctionName(self, index) > std::string const &  
def  updateParametersInContext 
Update the perparticle parameters in a Context to match those stored in this Force object.  
def  usesPeriodicBoundaryConditions 
usesPeriodicBoundaryConditions(self) > bool  
def  __init__ 
__init__(self, particlesPerSet, energy) > CustomManyParticleForce __init__(self, other) > CustomManyParticleForce  
Public Attributes  
this  
Static Public Attributes  
NoCutoff = _openmm.CustomManyParticleForce_NoCutoff  
CutoffNonPeriodic = _openmm.CustomManyParticleForce_CutoffNonPeriodic  
CutoffPeriodic = _openmm.CustomManyParticleForce_CutoffPeriodic  
SinglePermutation = _openmm.CustomManyParticleForce_SinglePermutation  
UniqueCentralParticle = _openmm.CustomManyParticleForce_UniqueCentralParticle 
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:
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 call addPerParticleParameter() to define perparticle parameters, and addGlobalParameter() 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 calling Context::setParameter().
Next, call addParticle() once for each particle in the System 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 the System, or else an exception will be thrown when you try to create a Context. After a particle has been added, you can modify its parameters by calling setParticleParameters(). This will have no effect on Contexts that already exist unless you call updateParametersInContext().
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, _all_ sets that include those two particles will be omitted.
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 _must_ be symmetric with respect to exchange of particles. Otherwise, the results would be undefined because permuting the labels would change 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 _any_ two particles are further apart than the cutoff distance, the interaction is skipped. In UniqueCentralParticle mode, each particle must be within the cutoff distance of the central particle, but not necessarily of all the other particles. The cutoff may therefore exclude a subset of the permutations of a set of particles.
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 _must_ be hydrogen and one of which _must_ be oxygen. Cases like this can be implemented using particle types.
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 call setTypeFilter() 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 a TabulatedFunction object. That function can then appear in the expression.
def __init__  (  self,  
args  
) 
__init__(self, particlesPerSet, energy) > CustomManyParticleForce __init__(self, other) > CustomManyParticleForce
Create a CustomManyParticleForce.
particlesPerSet  (int) the number of particles in each set for which the energy is evaluated 
energy  (string) 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 
def addExclusion  (  self,  
particle1,  
particle2  
) 
addExclusion(self, particle1, particle2) > int
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.
particle1  (int) the index of the first particle in the pair 
particle2  (int) the index of the second particle in the pair 
def addGlobalParameter  (  self,  
name,  
defaultValue  
) 
addGlobalParameter(self, name, defaultValue) > int
Add a new global parameter that the interaction may depend on.
name  (string) the name of the parameter 
defaultValue  (double) the default value of the parameter 
def addParticle  (  self,  
args  
) 
addParticle(self, parameters, type=0) > int addParticle(self, parameters) > int addParticle(self) > int
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  (vector< double >) the list of parameters for the new particle 
type  (int) the type of the new particle 
def addPerParticleParameter  (  self,  
name  
) 
addPerParticleParameter(self, name) > int
Add a new perparticle parameter that the interaction may depend on.
name  (string) the name of the parameter 
def addTabulatedFunction  (  self,  
name,  
function  
) 
addTabulatedFunction(self, name, function) > int
Add a tabulated function that may appear in the energy expression.
name  (string) the name of the function as it appears in expressions 
function  (TabulatedFunction *) a TabulatedFunction object defining the function. The TabulatedFunction should have been created on the heap with the "new" operator. The Force takes over ownership of it, and deletes it when the Force itself is deleted. 
def createExclusionsFromBonds  (  self,  
bonds,  
bondCutoff  
) 
Identify exclusions based on the molecular topology.
Particles which are separated by up to a specified number of bonds are added as exclusions.
bonds  (vector< std::pair< int, int > >) 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  (int) pairs of particles that are separated by this many bonds or fewer are added to the list of exclusions 
def getCutoffDistance  (  self  ) 
getCutoffDistance(self) > double
Get the cutoff distance (in nm) being used for nonbonded interactions. If the NonbondedMethod in use is NoCutoff, this value will have no effect.
def getEnergyFunction  (  self  ) 
getEnergyFunction(self) > std::string const &
Get the algebraic expression that gives the interaction energy of each bond
def getExclusionParticles  (  self,  
index  
) 
Get the particles in a pair whose interaction should be excluded.
index  (int) the index of the exclusion for which to get particle indices 
def getGlobalParameterDefaultValue  (  self,  
index  
) 
getGlobalParameterDefaultValue(self, index) > double
Get the default value of a global parameter.
index  (int) the index of the parameter for which to get the default value 
def getGlobalParameterName  (  self,  
index  
) 
getGlobalParameterName(self, index) > std::string const &
Get the name of a global parameter.
index  (int) the index of the parameter for which to get the name 
def getNonbondedMethod  (  self  ) 
getNonbondedMethod(self) > OpenMM::CustomManyParticleForce::NonbondedMethod
Get the method used for handling long range nonbonded interactions.
def getNumExclusions  (  self  ) 
getNumExclusions(self) > int
Get the number of particle pairs whose interactions should be excluded.
def getNumGlobalParameters  (  self  ) 
getNumGlobalParameters(self) > int
Get the number of global parameters that the interaction depends on.
def getNumParticles  (  self  ) 
getNumParticles(self) > int
Get the number of particles for which force field parameters have been defined.
def getNumParticlesPerSet  (  self  ) 
getNumParticlesPerSet(self) > int
Get the number of particles in each set for which the energy is evaluated
def getNumPerParticleParameters  (  self  ) 
getNumPerParticleParameters(self) > int
Get the number of perparticle parameters that the interaction depends on.
def getNumTabulatedFunctions  (  self  ) 
getNumTabulatedFunctions(self) > int
Get the number of tabulated functions that have been defined.
def getParticleParameters  (  self,  
index  
) 
Get the nonbonded force parameters for a particle.
index  (int) the index of the particle for which to get parameters 
def getPermutationMode  (  self  ) 
getPermutationMode(self) > OpenMM::CustomManyParticleForce::PermutationMode
Get the mode that selects which permutations of a set of particles to evaluate the interaction for.
def getPerParticleParameterName  (  self,  
index  
) 
getPerParticleParameterName(self, index) > std::string const &
Get the name of a perparticle parameter.
index  (int) the index of the parameter for which to get the name 
def getTabulatedFunction  (  self,  
args  
) 
getTabulatedFunction(self, index) > TabulatedFunction getTabulatedFunction(self, index) > TabulatedFunction
Get a reference to a tabulated function that may appear in the energy expression.
index  (int) the index of the function to get 
def getTabulatedFunctionName  (  self,  
index  
) 
getTabulatedFunctionName(self, index) > std::string const &
Get the name of a tabulated function that may appear in the energy expression.
index  (int) the index of the function to get 
def getTypeFilter  (  self,  
index  
) 
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.
index  (int) the index of the particle within the interaction (between 0 and getNumParticlesPerSet()) 
def setCutoffDistance  (  self,  
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.
distance  (double) the cutoff distance, measured in nm 
def setEnergyFunction  (  self,  
energy  
) 
Set the algebraic expression that gives the interaction energy of each bond.
def setExclusionParticles  (  self,  
index,  
particle1,  
particle2  
) 
Set the particles in a pair whose interaction should be excluded.
index  (int) the index of the exclusion for which to set particle indices 
particle1  (int) the index of the first particle in the pair 
particle2  (int) the index of the second particle in the pair 
def setGlobalParameterDefaultValue  (  self,  
index,  
defaultValue  
) 
Set the default value of a global parameter.
index  (int) the index of the parameter for which to set the default value 
defaultValue  (double) the default value of the parameter 
def setGlobalParameterName  (  self,  
index,  
name  
) 
Set the name of a global parameter.
index  (int) the index of the parameter for which to set the name 
name  (string) the name of the parameter 
def setNonbondedMethod  (  self,  
method  
) 
Set the method used for handling long range nonbonded interactions.
def setParticleParameters  (  self,  
index,  
parameters,  
type  
) 
Set the nonbonded force parameters for a particle.
index  (int) the index of the particle for which to set parameters 
parameters  (vector< double >) the list of parameters for the specified particle 
type  (int) the type of the specified particle 
def setPermutationMode  (  self,  
mode  
) 
Set the mode that selects which permutations of a set of particles to evaluate the interaction for.
def setPerParticleParameterName  (  self,  
index,  
name  
) 
Set the name of a perparticle parameter.
index  (int) the index of the parameter for which to set the name 
name  (string) the name of the parameter 
def setTypeFilter  (  self,  
index,  
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.
index  (int) the index of the particle within the interaction (between 0 and getNumParticlesPerSet()) 
types  (set< int >) the allowed types for the specified particle 
def updateParametersInContext  (  self,  
context  
) 
Update the perparticle parameters in a Context to match those stored in this Force object.
This method provides an efficient method to update certain parameters in an existing Context without needing to reinitialize it. Simply call setParticleParameters() to modify this object's parameters, then call updateParametersInContext() to copy them over to the Context.
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 the Context. Also, this method cannot be used to add new particles, only to change the parameters of existing ones.
def usesPeriodicBoundaryConditions  (  self  ) 
usesPeriodicBoundaryConditions(self) > bool
Returns whether or not this force makes use of periodic boundary conditions.
Reimplemented from Force.
CutoffNonPeriodic = _openmm.CustomManyParticleForce_CutoffNonPeriodic [static] 
CutoffPeriodic = _openmm.CustomManyParticleForce_CutoffPeriodic [static] 
NoCutoff = _openmm.CustomManyParticleForce_NoCutoff [static] 
SinglePermutation = _openmm.CustomManyParticleForce_SinglePermutation [static] 
UniqueCentralParticle = _openmm.CustomManyParticleForce_UniqueCentralParticle [static] 