NonbondedSoftcoreForce Class Reference
This class implements nonbonded interactions between particles, including a Coulomb force to represent electrostatics and a Lennard-Jones force to represent van der Waals interactions. More...
Public Member Functions | |
| def | getNumParticles |
| getNumParticles(self) -> int | |
| def | getNumExceptions |
| getNumExceptions(self) -> int | |
| def | getNonbondedMethod |
| getNonbondedMethod(self) -> NonbondedSoftcoreMethod | |
| def | setNonbondedMethod |
| setNonbondedMethod(self, NonbondedSoftcoreMethod method) | |
| def | getCutoffDistance |
| getCutoffDistance(self) -> double | |
| def | setCutoffDistance |
| setCutoffDistance(self, double distance) | |
| def | getReactionFieldDielectric |
| getReactionFieldDielectric(self) -> double | |
| def | setReactionFieldDielectric |
| setReactionFieldDielectric(self, double dielectric) | |
| def | addParticle |
| addParticle(self, double charge, double sigma, double epsilon, double softcoreLJLambda = 1.0) -> int addParticle(self, double charge, double sigma, double epsilon) -> int | |
| def | getParticleParameters |
| getParticleParameters(self, int index) | |
| def | setParticleParameters |
| setParticleParameters(self, int index, double charge, double sigma, double epsilon, double softcoreLJLambda = 1.0) setParticleParameters(self, int index, double charge, double sigma, double epsilon) | |
| def | addException |
| addException(self, int particle1, int particle2, double chargeProd, double sigma, double epsilon, bool replace = False, double softcoreLJLambda = 1.0) -> int addException(self, int particle1, int particle2, double chargeProd, double sigma, double epsilon, bool replace = False) -> int addException(self, int particle1, int particle2, double chargeProd, double sigma, double epsilon) -> int | |
| def | getExceptionParameters |
| getExceptionParameters(self, int index) | |
| def | setExceptionParameters |
| setExceptionParameters(self, int index, int particle1, int particle2, double chargeProd, double sigma, double epsilon, double softcoreLJLambda = 1.0) setExceptionParameters(self, int index, int particle1, int particle2, double chargeProd, double sigma, double epsilon) | |
| def | createExceptionsFromBonds |
| createExceptionsFromBonds(self, vectorpairii bonds, double coulomb14Scale, double lj14Scale) | |
| def | __init__ |
| __init__(self) -> NonbondedSoftcoreForce __init__(self, NonbondedSoftcoreForce other) -> NonbondedSoftcoreForce | |
| def | __del__ |
| __del__(self) | |
Public Attributes | |
| this | |
Static Public Attributes | |
| NoCutoff = _openmm.NonbondedSoftcoreForce_NoCutoff | |
| CutoffNonPeriodic = _openmm.NonbondedSoftcoreForce_CutoffNonPeriodic | |
| CutoffPeriodic = _openmm.NonbondedSoftcoreForce_CutoffPeriodic | |
Detailed Description
This class implements nonbonded interactions between particles, including a Coulomb force to represent electrostatics and a Lennard-Jones force to represent van der Waals interactions.
It optionally supports periodic boundary conditions and cutoffs for long range interactions. Lennard-Jones interactions are calculated with the Lorentz-Bertelot combining rule: it uses the arithmetic mean of the sigmas and the geometric mean of the epsilons for the two interacting particles.
To use this class, create a NonbondedSoftcoreForce object, then call addParticle() once for each particle in the System to define its parameters. The number of particles for which you define nonbonded 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 force field parameters by calling setParticleParameters().
NonbondedSoftcoreForce also lets you specify "exceptions", particular pairs of particles whose interactions should be computed based on different parameters than those defined for the individual particles. This can be used to completely exclude certain interactions from the force calculation, or to alter how they interact with each other.
Many molecular force fields omit Coulomb and Lennard-Jones interactions between particles separated by one or two bonds, while using modified parameters for those separated by three bonds (known as "1-4 interactions"). This class provides a convenience method for this case called createExceptionsFromBonds(). You pass to it a list of bonds and the scale factors to use for 1-4 interactions. It identifies all pairs of particles which are separated by 1, 2, or 3 bonds, then automatically creates exceptions for them.
Member Function Documentation
| def __del__ | ( | self | ) |
__del__(self)
Reimplemented from Force.
| def __init__ | ( | self, | ||
| args | ||||
| ) |
__init__(self) -> NonbondedSoftcoreForce __init__(self, NonbondedSoftcoreForce other) -> NonbondedSoftcoreForce
Create a NonbondedSoftcoreForce.
| def addException | ( | self, | ||
| args | ||||
| ) |
addException(self, int particle1, int particle2, double chargeProd, double sigma, double epsilon, bool replace = False, double softcoreLJLambda = 1.0) -> int addException(self, int particle1, int particle2, double chargeProd, double sigma, double epsilon, bool replace = False) -> int addException(self, int particle1, int particle2, double chargeProd, double sigma, double epsilon) -> int
Add an interaction to the list of exceptions that should be calculated differently from other interactions. If chargeProd and epsilon are both equal to 0, this will cause the interaction to be completely omitted from force and energy calculations.
In many cases, you can use createExceptionsFromBonds() rather than adding each exception explicitly.
- Parameters:
-
particle1 the index of the first particle involved in the interaction particle2 the index of the second particle involved in the interaction chargeProd the scaled product of the atomic charges (i.e. the strength of the Coulomb interaction), measured in units of the proton charge squared sigma the sigma parameter of the Lennard-Jones potential (corresponding to the van der Waals radius of the particle), measured in nm epsilon the epsilon parameter of the Lennard-Jones potential (corresponding to the well depth of the van der Waals interaction), measured in kJ/mol softcoreLJLambda the soft-core LJ parameter replace determines the behavior if there is already an exception for the same two particles. If true, the existing one is replaced. If false, an exception is thrown.
| def addParticle | ( | self, | ||
| args | ||||
| ) |
addParticle(self, double charge, double sigma, double epsilon, double softcoreLJLambda = 1.0) -> int addParticle(self, double charge, double sigma, double epsilon) -> 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. For calculating the Lennard-Jones interaction between two particles, the arithmetic mean of the sigmas and the geometric mean of the epsilons for the two interacting particles is used (the Lorentz-Bertelot combining rule).
- Parameters:
-
charge the charge of the particle, measured in units of the proton charge sigma the sigma parameter of the Lennard-Jones potential (corresponding to the van der Waals radius of the particle), measured in nm epsilon the epsilon parameter of the Lennard-Jones potential (corresponding to the well depth of the van der Waals interaction), measured in kJ/mol softcoreLJLambda the soft-core LJ parameter (default: 1.0)
| def createExceptionsFromBonds | ( | self, | ||
| args | ||||
| ) |
createExceptionsFromBonds(self, vectorpairii bonds, double coulomb14Scale, double lj14Scale)
Identify exceptions based on the molecular topology. Particles which are separated by one or two bonds are set to not interact at all, while pairs of particles separated by three bonds (known as "1-4 interactions") have their Coulomb and Lennard-Jones interactions reduced by a fixed factor.
- Parameters:
-
bonds the set of bonds based on which to construct exceptions. Each element specifies the indices of two particles that are bonded to each other. coulomb14Scale pairs of particles separated by three bonds will have the strength of their Coulomb interaction multiplied by this factor lj14Scale pairs of particles separated by three bonds will have the strength of their Lennard-Jones interaction multiplied by this factor
| 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 getExceptionParameters | ( | self, | ||
| args | ||||
| ) |
getExceptionParameters(self, int index)
Get the force field parameters for an interaction that should be calculated differently from others.
- Parameters:
-
index the index of the interaction for which to get parameters particle1 the index of the first particle involved in the interaction particle2 the index of the second particle involved in the interaction chargeProd the scaled product of the atomic charges (i.e. the strength of the Coulomb interaction), measured in units of the proton charge squared sigma the sigma parameter of the Lennard-Jones potential (corresponding to the van der Waals radius of the particle), measured in nm epsilon the epsilon parameter of the Lennard-Jones potential (corresponding to the well depth of the van der Waals interaction), measured in kJ/mol softcoreLJLambda the soft-core LJ parameter
| def getNonbondedMethod | ( | self | ) |
getNonbondedMethod(self) -> NonbondedSoftcoreMethod
Get the method used for handling long range nonbonded interactions.
| def getNumExceptions | ( | self | ) |
getNumExceptions(self) -> int
Get the number of special interactions that should be calculated differently from other interactions.
| def getNumParticles | ( | self | ) |
getNumParticles(self) -> int
Get the number of particles for which force field parameters have been defined.
| def getParticleParameters | ( | self, | ||
| args | ||||
| ) |
getParticleParameters(self, int index)
Get the nonbonded force parameters for a particle.
- Parameters:
-
index the index of the particle for which to get parameters charge the charge of the particle, measured in units of the proton charge sigma the sigma parameter of the Lennard-Jones potential (corresponding to the van der Waals radius of the particle), measured in nm epsilon the epsilon parameter of the Lennard-Jones potential (corresponding to the well depth of the van der Waals interaction), measured in kJ/mol softcoreLJLambda the soft-core LJ parameter
| def getReactionFieldDielectric | ( | self | ) |
getReactionFieldDielectric(self) -> double
Get the dielectric constant to use for the solvent in the reaction field approximation.
| def setCutoffDistance | ( | self, | ||
| args | ||||
| ) |
setCutoffDistance(self, 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.
| def setExceptionParameters | ( | self, | ||
| args | ||||
| ) |
setExceptionParameters(self, int index, int particle1, int particle2, double chargeProd, double sigma, double epsilon, double softcoreLJLambda = 1.0) setExceptionParameters(self, int index, int particle1, int particle2, double chargeProd, double sigma, double epsilon)
Set the force field parameters for an interaction that should be calculated differently from others. If chargeProd and epsilon are both equal to 0, this will cause the interaction to be completely omitted from force and energy calculations.
- Parameters:
-
index the index of the interaction for which to get parameters particle1 the index of the first particle involved in the interaction particle2 the index of the second particle involved in the interaction chargeProd the scaled product of the atomic charges (i.e. the strength of the Coulomb interaction), measured in units of the proton charge squared sigma the sigma parameter of the Lennard-Jones potential (corresponding to the van der Waals radius of the particle), measured in nm epsilon the epsilon parameter of the Lennard-Jones potential (corresponding to the well depth of the van der Waals interaction), measured in kJ/mol softcoreLJLambda the soft-core LJ parameter (default: 1.0)
| def setNonbondedMethod | ( | self, | ||
| args | ||||
| ) |
setNonbondedMethod(self, NonbondedSoftcoreMethod method)
Set the method used for handling long range nonbonded interactions.
| def setParticleParameters | ( | self, | ||
| args | ||||
| ) |
setParticleParameters(self, int index, double charge, double sigma, double epsilon, double softcoreLJLambda = 1.0) setParticleParameters(self, int index, double charge, double sigma, double epsilon)
Set the nonbonded force parameters for a particle. When calculating the Lennard-Jones interaction between two particles, it uses the arithmetic mean of the sigmas and the geometric mean of the epsilons for the two interacting particles (the Lorentz-Bertelot combining rule).
- Parameters:
-
index the index of the particle for which to set parameters charge the charge of the particle, measured in units of the proton charge sigma the sigma parameter of the Lennard-Jones potential (corresponding to the van der Waals radius of the particle), measured in nm epsilon the epsilon parameter of the Lennard-Jones potential (corresponding to the well depth of the van der Waals interaction), measured in kJ/mol softcoreLJLambda the soft-core LJ parameter (default: 1.0)
| def setReactionFieldDielectric | ( | self, | ||
| args | ||||
| ) |
setReactionFieldDielectric(self, double dielectric)
Set the dielectric constant to use for the solvent in the reaction field approximation.
Member Data Documentation
CutoffNonPeriodic = _openmm.NonbondedSoftcoreForce_CutoffNonPeriodic [static] |
CutoffPeriodic = _openmm.NonbondedSoftcoreForce_CutoffPeriodic [static] |
NoCutoff = _openmm.NonbondedSoftcoreForce_NoCutoff [static] |
The documentation for this class was generated from the following file:
- openmm.py
