AmoebaVdwForce

class simtk.openmm.openmm.AmoebaVdwForce(*args)

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.

__init__(self) → AmoebaVdwForce

__init__(self, other) -> AmoebaVdwForce

Create an Amoeba VdwForce.

Methods

__init__((self) -> AmoebaVdwForce) __init__(self, other) -> AmoebaVdwForce
addParticle((self, parentIndex, sigma, ...) Add the force field parameters for a vdw particle.
getCutoff((self) -> double) Get the cutoff distance.
getCutoffDistance((self) -> double) Get the cutoff distance (in nm) being used for nonbonded interactions.
getEpsilonCombiningRule(...) Get epsilon combining rule
getForceGroup((self) -> int) Get the force group this Force belongs to.
getNonbondedMethod(...) Get the method used for handling long range nonbonded interactions.
getNumParticles((self) -> int) Get the number of particles
getParticleExclusions(self, particleIndex) Get exclusions for specified particle
getParticleParameters(self, particleIndex) Get the force field parameters for a vdw particle.
getSigmaCombiningRule(...) Get sigma combining rule
getUseDispersionCorrection((self) -> bool) Get whether to add a contribution to the energy that approximately represents the effect of VdW interactions beyond the cutoff distance.
setCutoff(self, cutoff) Set the cutoff distance.
setCutoffDistance(self, distance) Set the cutoff distance (in nm) being used for nonbonded interactions.
setEpsilonCombiningRule(self, ...) Set epsilon combining rule
setForceGroup(self, group) Set the force group this Force belongs to.
setNonbondedMethod(self, method) Set the method used for handling long range nonbonded interactions.
setParticleExclusions(self, particleIndex, ...) Set exclusions for specified particle
setParticleParameters(self, particleIndex, ...) Set the force field parameters for a vdw particle.
setSigmaCombiningRule(self, sigmaCombiningRule) Set sigma combining rule
setUseDispersionCorrection(self, useCorrection) Set whether to add a contribution to the energy that approximately represents the effect of VdW interactions beyond the cutoff distance.
updateParametersInContext(self, context) Update the per-particle parameters in a Context to match those stored in this Force object.
usesPeriodicBoundaryConditions((self) -> bool) Returns whether or not this force makes use of periodic boundary conditions.

Attributes

CutoffPeriodic
NoCutoff
getNumParticles(self) → int

Get the number of particles

setParticleParameters(self, particleIndex, parentIndex, sigma, epsilon, reductionFactor)

Set the force field parameters for a vdw particle.

Parameters:
  • 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
getParticleParameters(self, particleIndex)

Get the force field parameters for a vdw particle.

Parameters:particleIndex (int) – the particle index
Returns:
  • 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
addParticle(self, parentIndex, sigma, epsilon, reductionFactor) → int

Add the force field parameters for a vdw particle.

Parameters:
  • 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
Returns:

index of added particle

Return type:

int

setSigmaCombiningRule(self, sigmaCombiningRule)

Set sigma combining rule

Parameters:sigmaCombiningRule (string) – sigma combining rule: ‘ARITHMETIC’, ‘GEOMETRIC’. ‘CUBIC-MEAN’
getSigmaCombiningRule(self) → std::string const &

Get sigma combining rule

Returns:sigmaCombiningRule sigma combining rule: ‘ARITHMETIC’, ‘GEOMETRIC’. ‘CUBIC-MEAN’
Return type:string
setEpsilonCombiningRule(self, epsilonCombiningRule)

Set epsilon combining rule

Parameters:epsilonCombiningRule (string) – epsilon combining rule: ‘ARITHMETIC’, ‘GEOMETRIC’. ‘HARMONIC’, ‘HHG’
getEpsilonCombiningRule(self) → std::string const &

Get epsilon combining rule

Returns:epsilonCombiningRule epsilon combining rule: ‘ARITHMETIC’, ‘GEOMETRIC’. ‘HARMONIC’, ‘HHG’
Return type:string
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.

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.

setParticleExclusions(self, particleIndex, exclusions)

Set exclusions for specified particle

Parameters:
  • particleIndex (int) – particle index
  • exclusions (vector< int >) – vector of exclusions
getParticleExclusions(self, particleIndex)

Get exclusions for specified particle

Parameters:particleIndex (int) – particle index
Returns:exclusions – vector of exclusions
Return type:vector< int >
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.

Returns:the cutoff distance, measured in nm
Return type:double
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.

Parameters:distance (double) – the cutoff distance, measured in nm
setCutoff(self, cutoff)

Set the cutoff distance.

Deprecated

This method exists only for backward compatibility. Use setCutoffDistance() instead.
getCutoff(self) → double

Get the cutoff distance.

Deprecated

This method exists only for backward compatibility. Use getCutoffDistance() instead.
getNonbondedMethod(self) → OpenMM::AmoebaVdwForce::NonbondedMethod

Get the method used for handling long range nonbonded interactions.

setNonbondedMethod(self, method)

Set the method used for handling long range nonbonded interactions.

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.

usesPeriodicBoundaryConditions(self) → bool

Returns whether or not this force makes use of periodic boundary conditions.

Returns:true if nonbondedMethod uses PBC and false otherwise
Return type:bool
__delattr__

x.__delattr__(‘name’) <==> del x.name

__format__()

default object formatter

__getattribute__

x.__getattribute__(‘name’) <==> x.name

__hash__
__reduce__()

helper for pickle

__reduce_ex__()

helper for pickle

__sizeof__() → int

size of object in memory, in bytes

__str__
getForceGroup(self) → int

Get the force group this Force belongs to.

setForceGroup(self, group)

Set the force group this Force belongs to.

Parameters:group (int) – the group index. Legal values are between 0 and 31 (inclusive).