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AmoebaVdwForce Class Reference

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(AmoebaVdwForce self) -> int More...
 
def setParticleParameters
 setParticleParameters(AmoebaVdwForce self, int particleIndex, int parentIndex, double sigma, double epsilon, double reductionFactor) More...
 
def getParticleParameters
 getParticleParameters(AmoebaVdwForce self, int particleIndex) More...
 
def addParticle
 addParticle(AmoebaVdwForce self, int parentIndex, double sigma, double epsilon, double reductionFactor) -> int More...
 
def setSigmaCombiningRule
 setSigmaCombiningRule(AmoebaVdwForce self, std::string const & sigmaCombiningRule) More...
 
def getSigmaCombiningRule
 getSigmaCombiningRule(AmoebaVdwForce self) -> std::string const & More...
 
def setEpsilonCombiningRule
 setEpsilonCombiningRule(AmoebaVdwForce self, std::string const & epsilonCombiningRule) More...
 
def getEpsilonCombiningRule
 getEpsilonCombiningRule(AmoebaVdwForce self) -> std::string const & More...
 
def getUseDispersionCorrection
 getUseDispersionCorrection(AmoebaVdwForce self) -> bool More...
 
def setUseDispersionCorrection
 setUseDispersionCorrection(AmoebaVdwForce self, bool useCorrection) More...
 
def setParticleExclusions
 setParticleExclusions(AmoebaVdwForce self, int particleIndex, vectori exclusions) More...
 
def getParticleExclusions
 getParticleExclusions(AmoebaVdwForce self, int particleIndex) More...
 
def setCutoff
 setCutoff(AmoebaVdwForce self, double cutoff) More...
 
def getCutoff
 getCutoff(AmoebaVdwForce self) -> double More...
 
def getNonbondedMethod
 getNonbondedMethod(AmoebaVdwForce self) -> OpenMM::AmoebaVdwForce::NonbondedMethod More...
 
def setNonbondedMethod
 setNonbondedMethod(AmoebaVdwForce self, OpenMM::AmoebaVdwForce::NonbondedMethod method) More...
 
def updateParametersInContext
 updateParametersInContext(AmoebaVdwForce self, Context context) More...
 
def __init__
 init(OpenMM::AmoebaVdwForce self) -> AmoebaVdwForce init(OpenMM::AmoebaVdwForce self, AmoebaVdwForce other) -> AmoebaVdwForce More...
 
def __del__
 del(OpenMM::AmoebaVdwForce self) More...
 
- Public Member Functions inherited from Force
def __init__
 
def __del__
 del(OpenMM::Force self) More...
 
def getForceGroup
 getForceGroup(Force self) -> int More...
 
def setForceGroup
 setForceGroup(Force self, int group) More...
 
def __copy__
 
def __deepcopy__
 

Public Attributes

 this
 

Static Public Attributes

 NoCutoff = _openmm.AmoebaVdwForce_NoCutoff
 
 CutoffPeriodic = _openmm.AmoebaVdwForce_CutoffPeriodic
 

Detailed Description

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.

Constructor & Destructor Documentation

def __init__ (   self,
  args 
)

init(OpenMM::AmoebaVdwForce self) -> AmoebaVdwForce init(OpenMM::AmoebaVdwForce self, AmoebaVdwForce other) -> AmoebaVdwForce

Create an Amoeba VdwForce.

References simtk.openmm.openmm.stripUnits().

def __del__ (   self)

del(OpenMM::AmoebaVdwForce self)

References simtk.openmm.openmm.stripUnits().

Member Function Documentation

def addParticle (   self,
  args 
)

addParticle(AmoebaVdwForce self, int parentIndex, double sigma, double epsilon, double reductionFactor) -> int

Add the force field parameters for a vdw particle.

Parameters
parentIndexthe index of the parent particle
sigmavdw sigma
epsilonvdw epsilon
reductionFactorthe fraction of the distance along the line from the parent particle to this particle at which the interaction site should be placed

References simtk.openmm.openmm.stripUnits().

Referenced by NonbondedForce.addParticle_usingRVdw().

def getCutoff (   self)

getCutoff(AmoebaVdwForce self) -> double

Get the cutoff distance.

References simtk.openmm.openmm.stripUnits().

def getEpsilonCombiningRule (   self)

getEpsilonCombiningRule(AmoebaVdwForce self) -> std::string const &

Get epsilon combining rule

References simtk.openmm.openmm.stripUnits().

def getNonbondedMethod (   self)

getNonbondedMethod(AmoebaVdwForce self) -> OpenMM::AmoebaVdwForce::NonbondedMethod

Get the method used for handling long range nonbonded interactions.

References simtk.openmm.openmm.stripUnits().

def getNumParticles (   self)

getNumParticles(AmoebaVdwForce self) -> int

Get the number of particles

References simtk.openmm.openmm.stripUnits().

def getParticleExclusions (   self,
  args 
)

getParticleExclusions(AmoebaVdwForce self, int particleIndex)

Get exclusions for specified particle

Parameters
particleIndexparticle index
exclusionsvector of exclusions

References simtk.openmm.openmm.stripUnits().

def getParticleParameters (   self,
  args 
)

getParticleParameters(AmoebaVdwForce self, int particleIndex)

Get the force field parameters for a vdw particle.

Parameters
particleIndexthe particle index
parentIndexthe index of the parent particle
sigmavdw sigma
epsilonvdw epsilon
reductionFactorthe fraction of the distance along the line from the parent particle to this particle at which the interaction site should be placed

References simtk.openmm.openmm.stripUnits().

def getSigmaCombiningRule (   self)

getSigmaCombiningRule(AmoebaVdwForce self) -> std::string const &

Get sigma combining rule

References simtk.openmm.openmm.stripUnits().

def getUseDispersionCorrection (   self)

getUseDispersionCorrection(AmoebaVdwForce 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.

References simtk.openmm.openmm.stripUnits().

def setCutoff (   self,
  args 
)

setCutoff(AmoebaVdwForce self, double cutoff)

Set the cutoff distance.

References simtk.openmm.openmm.stripUnits().

def setEpsilonCombiningRule (   self,
  args 
)

setEpsilonCombiningRule(AmoebaVdwForce self, std::string const & epsilonCombiningRule)

Set epsilon combining rule

Parameters
epsilonCombiningRuleepsilon combining rule: 'ARITHMETIC', 'GEOMETRIC'. 'HARMONIC', 'HHG'

References simtk.openmm.openmm.stripUnits().

def setNonbondedMethod (   self,
  args 
)

setNonbondedMethod(AmoebaVdwForce self, OpenMM::AmoebaVdwForce::NonbondedMethod method)

Set the method used for handling long range nonbonded interactions.

References simtk.openmm.openmm.stripUnits().

def setParticleExclusions (   self,
  args 
)

setParticleExclusions(AmoebaVdwForce self, int particleIndex, vectori exclusions)

Set exclusions for specified particle

Parameters
particleIndexparticle index
exclusionsvector of exclusions

References simtk.openmm.openmm.stripUnits().

def setParticleParameters (   self,
  args 
)

setParticleParameters(AmoebaVdwForce self, int particleIndex, int parentIndex, double sigma, double epsilon, double reductionFactor)

Set the force field parameters for a vdw particle.

Parameters
particleIndexthe particle index
parentIndexthe index of the parent particle
sigmavdw sigma
epsilonvdw epsilon
reductionFactorthe fraction of the distance along the line from the parent particle to this particle at which the interaction site should be placed

References simtk.openmm.openmm.stripUnits().

def setSigmaCombiningRule (   self,
  args 
)

setSigmaCombiningRule(AmoebaVdwForce self, std::string const & sigmaCombiningRule)

Set sigma combining rule

Parameters
sigmaCombiningRulesigma combining rule: 'ARITHMETIC', 'GEOMETRIC'. 'CUBIC-MEAN'

References simtk.openmm.openmm.stripUnits().

def setUseDispersionCorrection (   self,
  args 
)

setUseDispersionCorrection(AmoebaVdwForce self, bool 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.

References simtk.openmm.openmm.stripUnits().

def updateParametersInContext (   self,
  args 
)

updateParametersInContext(AmoebaVdwForce self, Context 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 updateParametersInState() 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.

References simtk.openmm.openmm.stripUnits().

Member Data Documentation

CutoffPeriodic = _openmm.AmoebaVdwForce_CutoffPeriodic
static
NoCutoff = _openmm.AmoebaVdwForce_NoCutoff
static
this

Referenced by System.__init__().


The documentation for this class was generated from the following file: