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

__copy__(self) → Force¶

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).