AmoebaVdwForce¶

class
OpenMM::
AmoebaVdwForce
¶ This class implements a buffered 147 potential used to model van der Waals forces.
To use it, create an
AmoebaVdwForce
object then calladdParticle()
once for each particle. After a particle has been added, you can modify its force field parameters by callingsetParticleParameters()
. This will have no effect on Contexts that already exist unless you callupdateParametersInContext()
.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 perparticle parameters in a Context
to match those stored in thisForce
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’. ‘CUBICMEAN’

const std::string &
getSigmaCombiningRule
(void) const¶ Get sigma combining rule
Returns: sigmaCombiningRule sigma combining rule: ‘ARITHMETIC’, ‘GEOMETRIC’. ‘CUBICMEAN’

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

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.
Parameters:  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 perparticle parameters in a
Context
to match those stored in thisForce
object. This method provides an efficient method to update certain parameters in an existingContext
without needing to reinitialize it. Simply callsetParticleParameters()
to modify this object’s parameters, then callupdateParametersInContext()
to copy them over to theContext
.The only information this method updates is the values of perparticle parameters. All other aspects of the
Force
(the nonbonded method, the cutoff distance, etc.) are unaffected and can only be changed by reinitializing theContext
.

bool
usesPeriodicBoundaryConditions
() const¶ Returns whether or not this force makes use of periodic boundary conditions.
Returns: true if nonbondedMethod uses PBC and false otherwise
