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OpenMM
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OpenMM
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This class implements a buffered 14-7 potential used to model van der Waals forces. More...
Inheritance diagram for AmoebaVdwForce:Public Member Functions | |
| def | getNumParticles |
| getNumParticles(self) -> int | |
| def | setParticleParameters |
| Set the force field parameters for a vdw particle. | |
| def | getParticleParameters |
| Get the force field parameters for a vdw particle. | |
| def | addParticle |
| addParticle(self, parentIndex, sigma, epsilon, reductionFactor) -> int | |
| def | setSigmaCombiningRule |
| Set sigma combining rule. | |
| def | getSigmaCombiningRule |
| getSigmaCombiningRule(self) -> std::string const & | |
| def | setEpsilonCombiningRule |
| Set epsilon combining rule. | |
| def | getEpsilonCombiningRule |
| getEpsilonCombiningRule(self) -> std::string const & | |
| def | getUseDispersionCorrection |
| getUseDispersionCorrection(self) -> bool | |
| def | setUseDispersionCorrection |
| Set whether to add a contribution to the energy that approximately represents the effect of VdW interactions beyond the cutoff distance. | |
| def | setParticleExclusions |
| Set exclusions for specified particle. | |
| def | getParticleExclusions |
| Get exclusions for specified particle. | |
| def | setCutoff |
| Set the cutoff distance. | |
| def | getCutoff |
| getCutoff(self) -> double | |
| def | getNonbondedMethod |
| getNonbondedMethod(self) -> OpenMM::AmoebaVdwForce::NonbondedMethod | |
| def | setNonbondedMethod |
| Set the method used for handling long range nonbonded interactions. | |
| def | updateParametersInContext |
| Update the per-particle parameters in a Context to match those stored in this Force object. | |
| def | usesPeriodicBoundaryConditions |
| usesPeriodicBoundaryConditions(self) -> bool | |
| def | __init__ |
| __init__(self) -> AmoebaVdwForce __init__(self, other) -> AmoebaVdwForce | |
Public Attributes | |
| this | |
Static Public Attributes | |
| NoCutoff = _openmm.AmoebaVdwForce_NoCutoff | |
| CutoffPeriodic = _openmm.AmoebaVdwForce_CutoffPeriodic | |
This class implements a buffered 14-7 potential used to model van der Waals forces.
To use it, create an AmoebaVdwForce object then call addParticle() once for each particle. After a particle has been added, you can modify its force field parameters by calling setParticleParameters(). This will have no effect on Contexts that already exist unless you call updateParametersInContext().
A unique feature of this class is that the interaction site for a particle does not need to be exactly at the particle's location. Instead, it can be placed a fraction of the distance from that particle to another one. This is typically done for hydrogens to place the interaction site slightly closer to the parent atom. The fraction is known as the "reduction factor", since it reduces the distance from the parent atom to the interaction site.
| def __init__ | ( | self, | |
| args | |||
| ) |
__init__(self) -> AmoebaVdwForce __init__(self, other) -> AmoebaVdwForce
Create an Amoeba VdwForce.
| def addParticle | ( | self, | |
| parentIndex, | |||
| sigma, | |||
| epsilon, | |||
| reductionFactor | |||
| ) |
addParticle(self, parentIndex, sigma, epsilon, reductionFactor) -> int
Add the force field parameters for a vdw particle.
| parentIndex | (int) the index of the parent particle |
| sigma | (double) vdw sigma |
| epsilon | (double) vdw epsilon |
| reductionFactor | (double) the fraction of the distance along the line from the parent particle to this particle at which the interaction site should be placed |
| def getCutoff | ( | self | ) |
getCutoff(self) -> double
Get the cutoff distance.
| def getEpsilonCombiningRule | ( | self | ) |
getEpsilonCombiningRule(self) -> std::string const &
Get epsilon combining rule
| def getNonbondedMethod | ( | self | ) |
getNonbondedMethod(self) -> OpenMM::AmoebaVdwForce::NonbondedMethod
Get the method used for handling long range nonbonded interactions.
| def getNumParticles | ( | self | ) |
getNumParticles(self) -> int
Get the number of particles
| def getParticleExclusions | ( | self, | |
| particleIndex | |||
| ) |
Get exclusions for specified particle.
| particleIndex | (int) particle index |
| def getParticleParameters | ( | self, | |
| particleIndex | |||
| ) |
Get the force field parameters for a vdw particle.
| particleIndex | (int) the particle index |
| def getSigmaCombiningRule | ( | self | ) |
getSigmaCombiningRule(self) -> std::string const &
Get sigma combining rule
| def getUseDispersionCorrection | ( | self | ) |
getUseDispersionCorrection(self) -> bool
Get whether to add a contribution to the energy that approximately represents the effect of VdW interactions beyond the cutoff distance. The energy depends on the volume of the periodic box, and is only applicable when periodic boundary conditions are used. When running simulations at constant pressure, adding this contribution can improve the quality of results.
| def setCutoff | ( | self, | |
| cutoff | |||
| ) |
Set the cutoff distance.
| def setEpsilonCombiningRule | ( | self, | |
| epsilonCombiningRule | |||
| ) |
Set epsilon combining rule.
| epsilonCombiningRule | (string) epsilon combining rule: 'ARITHMETIC', 'GEOMETRIC'. 'HARMONIC', 'HHG' |
| def setNonbondedMethod | ( | self, | |
| method | |||
| ) |
Set the method used for handling long range nonbonded interactions.
| def setParticleExclusions | ( | self, | |
| particleIndex, | |||
| exclusions | |||
| ) |
Set exclusions for specified particle.
| particleIndex | (int) particle index |
| exclusions | (vector< int >) vector of exclusions |
| def setParticleParameters | ( | self, | |
| particleIndex, | |||
| parentIndex, | |||
| sigma, | |||
| epsilon, | |||
| reductionFactor | |||
| ) |
Set the force field parameters for a vdw particle.
| particleIndex | (int) the particle index |
| parentIndex | (int) the index of the parent particle |
| sigma | (double) vdw sigma |
| epsilon | (double) vdw epsilon |
| reductionFactor | (double) the fraction of the distance along the line from the parent particle to this particle at which the interaction site should be placed |
| def setSigmaCombiningRule | ( | self, | |
| sigmaCombiningRule | |||
| ) |
Set sigma combining rule.
| sigmaCombiningRule | (string) sigma combining rule: 'ARITHMETIC', 'GEOMETRIC'. 'CUBIC-MEAN' |
| def setUseDispersionCorrection | ( | self, | |
| useCorrection | |||
| ) |
Set whether to add a contribution to the energy that approximately represents the effect of VdW interactions beyond the cutoff distance.
The energy depends on the volume of the periodic box, and is only applicable when periodic boundary conditions are used. When running simulations at constant pressure, adding this contribution can improve the quality of results.
| def updateParametersInContext | ( | self, | |
| context | |||
| ) |
Update the per-particle 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.
The only information this method updates is the values of per-particle parameters. All other aspects of the Force (the nonbonded method, the cutoff distance, etc.) are unaffected and can only be changed by reinitializing the Context.
| def usesPeriodicBoundaryConditions | ( | self | ) |
usesPeriodicBoundaryConditions(self) -> bool
Returns whether or not this force makes use of periodic boundary conditions.
Reimplemented from Force.
CutoffPeriodic = _openmm.AmoebaVdwForce_CutoffPeriodic [static] |
NoCutoff = _openmm.AmoebaVdwForce_NoCutoff [static] |
1.7.6.1 
