# 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 getCutoffDistance Get the cutoff distance (in nm) being used for nonbonded interactions. setCutoffDistance Set the cutoff distance (in nm) being used for nonbonded interactions. 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.

• 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.

• 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.

• 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

• 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

• 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

• particleIndex – particle index
• exclusions – vector of exclusions
void getParticleExclusions(int particleIndex, std::vector<int> &exclusions) const

Get exclusions for specified particle

• particleIndex – particle index
• exclusions – [out] vector of exclusions
double getCutoffDistance() const

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
void setCutoffDistance(double 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.

• distance – the cutoff distance, measured in nm
void setCutoff(double cutoff)

Set the cutoff distance.

Deprecated

This method exists only for backward compatibility. Use setCutoffDistance() instead.

double getCutoff() const

Get the cutoff distance.

Deprecated

This method exists only for backward compatibility. Use getCutoffDistance() instead.

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