AmoebaVdwForce¶

class OpenMM::AmoebaVdwForce¶

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.

Methods

`AmoebaVdwForce()`	Create an Amoeba VdwForce.
`getNumParticles()`	Get the number of particles
`setParticleParameters()`	Set the force field parameters for a vdw particle.
`getParticleParameters()`	Get the force field parameters for a vdw particle.
`addParticle()`	Add the force field parameters for a vdw particle.
`setSigmaCombiningRule()`	Set sigma combining rule
`getSigmaCombiningRule()`	Get sigma combining rule
`setEpsilonCombiningRule()`	Set epsilon combining rule
`getEpsilonCombiningRule()`	Get epsilon combining rule
`getUseDispersionCorrection()`	Get whether to add a contribution to the energy that approximately represents the effect of VdW interactions beyond the cutoff distance.
`setUseDispersionCorrection()`	Set whether to add a contribution to the energy that approximately represents the effect of VdW interactions beyond the cutoff distance.
`setParticleExclusions()`	Set exclusions for specified particle
`getParticleExclusions()`	Get exclusions for specified particle
`setCutoff()`	Set the cutoff distance.
`getCutoff()`	Get the cutoff distance.
`getNonbondedMethod()`	Get the method used for handling long range nonbonded interactions.
`setNonbondedMethod()`	Set the method used for handling long range nonbonded interactions.
`updateParametersInContext()`	Update the per-particle parameters in a `Context` to match those stored in this `Force` object.
`usesPeriodicBoundaryConditions()`	Returns whether or not this force makes use of periodic boundary conditions.

Enum: NonbondedMethod

NoCutoff	No cutoff is applied to nonbonded interactions. The full set of N^2 interactions is computed exactly. This necessarily means that periodic boundary conditions cannot be used. This is the default.
CutoffPeriodic	Periodic boundary conditions are used, so that each particle interacts only with the nearest periodic copy of each other particle. Interactions beyond the cutoff distance are ignored.

AmoebaVdwForce()¶: Create an Amoeba VdwForce.

int getNumParticles() const¶: Get the number of particles

void setParticleParameters(int particleIndex, int parentIndex, double sigma, double epsilon, double reductionFactor)¶

Set the force field parameters for a vdw particle.

Parameters:

particleIndex – the particle index
parentIndex – the index of the parent particle
sigma – vdw sigma
epsilon – vdw epsilon
reductionFactor – the fraction of the distance along the line from the parent particle to this particle at which the interaction site should be placed

void getParticleParameters(int particleIndex, int &parentIndex, double &sigma, double &epsilon, double &reductionFactor) const¶

Get the force field parameters for a vdw particle.

Parameters:

particleIndex – the particle index
parentIndex – [out] the index of the parent particle
sigma – [out] vdw sigma
epsilon – [out] vdw epsilon
reductionFactor – [out] the fraction of the distance along the line from the parent particle to this particle at which the interaction site should be placed

int addParticle(int parentIndex, double sigma, double epsilon, double reductionFactor)¶

Add the force field parameters for a vdw particle.

Parameters:

parentIndex – the index of the parent particle
sigma – vdw sigma
epsilon – vdw epsilon
reductionFactor – 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

void setSigmaCombiningRule(const std::string &sigmaCombiningRule)¶

Set sigma combining rule

Parameters:

sigmaCombiningRule – sigma combining rule: ‘ARITHMETIC’, ‘GEOMETRIC’. ‘CUBIC-MEAN’

const std::string &getSigmaCombiningRule(void) const¶

Get sigma combining rule

Returns:	sigmaCombiningRule sigma combining rule: ‘ARITHMETIC’, ‘GEOMETRIC’. ‘CUBIC-MEAN’

void setEpsilonCombiningRule(const std::string &epsilonCombiningRule)¶

Set epsilon combining rule

Parameters:

epsilonCombiningRule – epsilon combining rule: ‘ARITHMETIC’, ‘GEOMETRIC’. ‘HARMONIC’, ‘HHG’

const std::string &getEpsilonCombiningRule(void) const¶

Get epsilon combining rule

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

bool getUseDispersionCorrection() const¶: 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.

void setUseDispersionCorrection(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.

void setParticleExclusions(int particleIndex, const std::vector<int> &exclusions)¶

Set exclusions for specified particle

Parameters:

particleIndex – particle index
exclusions – vector of exclusions

void getParticleExclusions(int particleIndex, std::vector<int> &exclusions) const¶

Get exclusions for specified particle

Parameters:

particleIndex – particle index
exclusions – [out] vector of exclusions

void setCutoff(double cutoff)¶: Set the cutoff distance.

double getCutoff() const¶: Get the cutoff distance.

NonbondedMethod getNonbondedMethod() const¶: Get the method used for handling long range nonbonded interactions.

void setNonbondedMethod(NonbondedMethod method)¶: Set the method used for handling long range nonbonded interactions.

void updateParametersInContext(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 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.

bool usesPeriodicBoundaryConditions() const¶

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

Returns:	true if nonbondedMethod uses PBC and false otherwise