`NonbondedForce`¶

class OpenMM::NonbondedForce : public OpenMM::Force ¶

This class implements nonbonded interactions between particles, including a Coulomb force to represent electrostatics and a Lennard-Jones force to represent van der Waals interactions. It optionally supports periodic boundary conditions and cutoffs for long range interactions. Lennard-Jones interactions are calculated with the Lorentz-Berthelot combining rule: it uses the arithmetic mean of the sigmas and the geometric mean of the epsilons for the two interacting particles.

To use this class, create a NonbondedForce object, then call addParticle() once for each particle in the System to define its parameters. The number of particles for which you define nonbonded parameters must be exactly equal to the number of particles in the System, or else an exception will be thrown when you try to create a Context. 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().

NonbondedForce also lets you specify “exceptions”, particular pairs of particles whose interactions should be computed based on different parameters than those defined for the individual particles. This can be used to completely exclude certain interactions from the force calculation, or to alter how they interact with each other.

Many molecular force fields omit Coulomb and Lennard-Jones interactions between particles separated by one or two bonds, while using modified parameters for those separated by three bonds (known as “1-4 interactions”). This class provides a convenience method for this case called createExceptionsFromBonds(). You pass to it a list of bonds and the scale factors to use for 1-4 interactions. It identifies all pairs of particles which are separated by 1, 2, or 3 bonds, then automatically creates exceptions for them.

When using a cutoff, by default Lennard-Jones interactions are sharply truncated at the cutoff distance. Optionally you can instead use a switching function to make the interaction smoothly go to zero over a finite distance range. To enable this, call setUseSwitchingFunction(). You must also call setSwitchingDistance() to specify the distance at which the interaction should begin to decrease. The switching distance must be less than the cutoff distance.

Another optional feature of this class (enabled by default) is to add a contribution to the energy which approximates the effect of all Lennard-Jones interactions beyond the cutoff in a periodic system. When running a simulation at constant pressure, this can improve the quality of the result. Call setUseDispersionCorrection() to set whether this should be used.

In some applications, it is useful to be able to inexpensively change the parameters of small groups of particles. Usually this is done to interpolate between two sets of parameters. For example, a titratable group might have two states it can exist in, each described by a different set of parameters for the atoms that make up the group. You might then want to smoothly interpolate between the two states. This is done by first calling addGlobalParameter() to define a Context parameter, then addParticleParameterOffset() to create a “parameter offset” that depends on the Context parameter. Each offset defines the following:

A Context parameter used to interpolate between the states.
A single particle whose parameters are influenced by the Context parameter.
Three scale factors (chargeScale, sigmaScale, and epsilonScale) that specify how the Context parameter affects the particle.

The “effective” parameters for a particle (those used to compute forces) are given by

charge = baseCharge + param*chargeScale
sigma = baseSigma + param*sigmaScale
epsilon = baseEpsilon + param*epsilonScale

where the “base” values are the ones specified by addParticle() and “oaram” is the current value of the Context parameter. A single Context parameter can apply offsets to multiple particles, and multiple parameters can be used to apply offsets to the same particle. Parameters can also be used to modify exceptions in exactly the same way by calling addExceptionParameterOffset().

Public Types

enum NonbondedMethod¶

This is an enumeration of the different methods that may be used for handling long range nonbonded forces.

Values:

enumerator 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.

enumerator CutoffNonPeriodic¶: Interactions beyond the cutoff distance are ignored. Coulomb interactions closer than the cutoff distance are modified using the reaction field method.

enumerator 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. Coulomb interactions closer than the cutoff distance are modified using the reaction field method.

enumerator Ewald¶: Periodic boundary conditions are used, and Ewald summation is used to compute the Coulomb interaction of each particle with all periodic copies of every other particle.

enumerator PME¶: Periodic boundary conditions are used, and Particle-Mesh Ewald (PME) summation is used to compute the Coulomb interaction of each particle with all periodic copies of every other particle.

enumerator LJPME¶: Periodic boundary conditions are used, and Particle-Mesh Ewald (PME) summation is used to compute the interaction of each particle with all periodic copies of every other particle for both Coulomb and Lennard-Jones. No switching is used for either interaction.

Public Functions

NonbondedForce()¶: Create a NonbondedForce.

inline int getNumParticles() const¶: Get the number of particles for which force field parameters have been defined.

inline int getNumExceptions() const¶: Get the number of special interactions that should be calculated differently from other interactions.

inline int getNumGlobalParameters() const¶: Get the number of global parameters that have been added.

inline int getNumParticleParameterOffsets() const¶: Get the number of particles parameter offsets that have been added.

inline int getNumExceptionParameterOffsets() const¶: Get the number of exception parameter offsets that have been added.

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.

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

bool getUseSwitchingFunction() const¶: Get whether a switching function is applied to the Lennard-Jones interaction. If the nonbonded method is set to NoCutoff, this option is ignored.

void setUseSwitchingFunction(bool use)¶: Set whether a switching function is applied to the Lennard-Jones interaction. If the nonbonded method is set to NoCutoff, this option is ignored.

double getSwitchingDistance() const¶: Get the distance at which the switching function begins to reduce the Lennard-Jones interaction. This must be less than the cutoff distance.

void setSwitchingDistance(double distance)¶: Set the distance at which the switching function begins to reduce the Lennard-Jones interaction. This must be less than the cutoff distance.

double getReactionFieldDielectric() const¶: Get the dielectric constant to use for the solvent in the reaction field approximation.

void setReactionFieldDielectric(double dielectric)¶: Set the dielectric constant to use for the solvent in the reaction field approximation.

double getEwaldErrorTolerance() const¶

Get the error tolerance for Ewald summation. This corresponds to the fractional error in the forces which is acceptable. This value is used to select the reciprocal space cutoff and separation parameter so that the average error level will be less than the tolerance. There is not a rigorous guarantee that all forces on all atoms will be less than the tolerance, however.

For PME calculations, if setPMEParameters() is used to set alpha to something other than 0, this value is ignored.

void setEwaldErrorTolerance(double tol)¶

Set the error tolerance for Ewald summation. This corresponds to the fractional error in the forces which is acceptable. This value is used to select the reciprocal space cutoff and separation parameter so that the average error level will be less than the tolerance. There is not a rigorous guarantee that all forces on all atoms will be less than the tolerance, however.

For PME calculations, if setPMEParameters() is used to set alpha to something other than 0, this value is ignored.

void getPMEParameters(double &alpha, int &nx, int &ny, int &nz) const¶

Get the parameters to use for PME calculations. If alpha is 0 (the default), these parameters are ignored and instead their values are chosen based on the Ewald error tolerance.

Parameters

alpha – [out] the separation parameter
nx – [out] the number of grid points along the X axis
ny – [out] the number of grid points along the Y axis
nz – [out] the number of grid points along the Z axis

void getLJPMEParameters(double &alpha, int &nx, int &ny, int &nz) const¶

Get the parameters to use for dispersion term in LJ-PME calculations. If alpha is 0 (the default), these parameters are ignored and instead their values are chosen based on the Ewald error tolerance.

Parameters

alpha – [out] the separation parameter
nx – [out] the number of dispersion grid points along the X axis
ny – [out] the number of dispersion grid points along the Y axis
nz – [out] the number of dispersion grid points along the Z axis

void setPMEParameters(double alpha, int nx, int ny, int nz)¶

Set the parameters to use for PME calculations. If alpha is 0 (the default), these parameters are ignored and instead their values are chosen based on the Ewald error tolerance.

Parameters

alpha – the separation parameter
nx – the number of grid points along the X axis
ny – the number of grid points along the Y axis
nz – the number of grid points along the Z axis

void setLJPMEParameters(double alpha, int nx, int ny, int nz)¶

Set the parameters to use for the dispersion term in LJPME calculations. If alpha is 0 (the default), these parameters are ignored and instead their values are chosen based on the Ewald error tolerance.

Parameters

alpha – the separation parameter
nx – the number of grid points along the X axis
ny – the number of grid points along the Y axis
nz – the number of grid points along the Z axis

void getPMEParametersInContext(const Context &context, double &alpha, int &nx, int &ny, int &nz) const¶

Get the parameters being used for PME in a particular Context. Because some platforms have restrictions on the allowed grid sizes, the values that are actually used may be slightly different from those specified with setPMEParameters(), or the standard values calculated based on the Ewald error tolerance. See the manual for details.

Parameters

context – the Context for which to get the parameters
alpha – [out] the separation parameter
nx – [out] the number of grid points along the X axis
ny – [out] the number of grid points along the Y axis
nz – [out] the number of grid points along the Z axis

void getLJPMEParametersInContext(const Context &context, double &alpha, int &nx, int &ny, int &nz) const¶

Get the PME parameters being used for the dispersion term for LJPME in a particular Context. Because some platforms have restrictions on the allowed grid sizes, the values that are actually used may be slightly different from those specified with setPMEParameters(), or the standard values calculated based on the Ewald error tolerance. See the manual for details.

Parameters

context – the Context for which to get the parameters
alpha – [out] the separation parameter
nx – [out] the number of grid points along the X axis
ny – [out] the number of grid points along the Y axis
nz – [out] the number of grid points along the Z axis

int addParticle(double charge, double sigma, double epsilon)¶

Add the nonbonded force parameters for a particle. This should be called once for each particle in the System. When it is called for the i’th time, it specifies the parameters for the i’th particle. For calculating the Lennard-Jones interaction between two particles, the arithmetic mean of the sigmas and the geometric mean of the epsilons for the two interacting particles is used (the Lorentz-Berthelot combining rule).

Parameters

charge – the charge of the particle, measured in units of the proton charge
sigma – the sigma parameter of the Lennard-Jones potential (corresponding to the van der Waals radius of the particle), measured in nm
epsilon – the epsilon parameter of the Lennard-Jones potential (corresponding to the well depth of the van der Waals interaction), measured in kJ/mol

Returns

the index of the particle that was added

void getParticleParameters(int index, double &charge, double &sigma, double &epsilon) const¶

Get the nonbonded force parameters for a particle.

Parameters

index – the index of the particle for which to get parameters
charge – [out] the charge of the particle, measured in units of the proton charge
sigma – [out] the sigma parameter of the Lennard-Jones potential (corresponding to the van der Waals radius of the particle), measured in nm
epsilon – [out] the epsilon parameter of the Lennard-Jones potential (corresponding to the well depth of the van der Waals interaction), measured in kJ/mol

void setParticleParameters(int index, double charge, double sigma, double epsilon)¶

Set the nonbonded force parameters for a particle. When calculating the Lennard-Jones interaction between two particles, it uses the arithmetic mean of the sigmas and the geometric mean of the epsilons for the two interacting particles (the Lorentz-Berthelot combining rule).

Parameters

index – the index of the particle for which to set parameters
charge – the charge of the particle, measured in units of the proton charge
sigma – the sigma parameter of the Lennard-Jones potential (corresponding to the van der Waals radius of the particle), measured in nm
epsilon – the epsilon parameter of the Lennard-Jones potential (corresponding to the well depth of the van der Waals interaction), measured in kJ/mol

int addException(int particle1, int particle2, double chargeProd, double sigma, double epsilon, bool replace = false)¶

Add an interaction to the list of exceptions that should be calculated differently from other interactions. If chargeProd and epsilon are both equal to 0, this will cause the interaction to be completely omitted from force and energy calculations.

In many cases, you can use createExceptionsFromBonds() rather than adding each exception explicitly.

Parameters

particle1 – the index of the first particle involved in the interaction
particle2 – the index of the second particle involved in the interaction
chargeProd – the scaled product of the atomic charges (i.e. the strength of the Coulomb interaction), measured in units of the proton charge squared
sigma – the sigma parameter of the Lennard-Jones potential (corresponding to the van der Waals radius of the particle), measured in nm
epsilon – the epsilon parameter of the Lennard-Jones potential (corresponding to the well depth of the van der Waals interaction), measured in kJ/mol
replace – determines the behavior if there is already an exception for the same two particles. If true, the existing one is replaced. If false, an exception is thrown.

Returns

the index of the exception that was added

void getExceptionParameters(int index, int &particle1, int &particle2, double &chargeProd, double &sigma, double &epsilon) const¶

Get the force field parameters for an interaction that should be calculated differently from others.

Parameters

index – the index of the interaction for which to get parameters
particle1 – [out] the index of the first particle involved in the interaction
particle2 – [out] the index of the second particle involved in the interaction
chargeProd – [out] the scaled product of the atomic charges (i.e. the strength of the Coulomb interaction), measured in units of the proton charge squared
sigma – [out] the sigma parameter of the Lennard-Jones potential (corresponding to the van der Waals radius of the particle), measured in nm
epsilon – [out] the epsilon parameter of the Lennard-Jones potential (corresponding to the well depth of the van der Waals interaction), measured in kJ/mol

void setExceptionParameters(int index, int particle1, int particle2, double chargeProd, double sigma, double epsilon)¶

Set the force field parameters for an interaction that should be calculated differently from others. If chargeProd and epsilon are both equal to 0, this will cause the interaction to be completely omitted from force and energy calculations.

Parameters

index – the index of the interaction for which to get parameters
particle1 – the index of the first particle involved in the interaction
particle2 – the index of the second particle involved in the interaction
chargeProd – the scaled product of the atomic charges (i.e. the strength of the Coulomb interaction), measured in units of the proton charge squared
sigma – the sigma parameter of the Lennard-Jones potential (corresponding to the van der Waals radius of the particle), measured in nm
epsilon – the epsilon parameter of the Lennard-Jones potential (corresponding to the well depth of the van der Waals interaction), measured in kJ/mol

void createExceptionsFromBonds(const std::vector<std::pair<int, int>> &bonds, double coulomb14Scale, double lj14Scale)¶

Identify exceptions based on the molecular topology. Particles which are separated by one or two bonds are set to not interact at all, while pairs of particles separated by three bonds (known as “1-4 interactions”) have their Coulomb and Lennard-Jones interactions reduced by a fixed factor.

Parameters

bonds – the set of bonds based on which to construct exceptions. Each element specifies the indices of two particles that are bonded to each other.
coulomb14Scale – pairs of particles separated by three bonds will have the strength of their Coulomb interaction multiplied by this factor
lj14Scale – pairs of particles separated by three bonds will have the strength of their Lennard-Jones interaction multiplied by this factor

int addGlobalParameter(const std::string &name, double defaultValue)¶

Add a new global parameter that parameter offsets may depend on. The default value provided to this method is the initial value of the parameter in newly created Contexts. You can change the value at any time by calling setParameter() on the Context.

Parameters

name – the name of the parameter
defaultValue – the default value of the parameter

Returns

the index of the parameter that was added

const std::string &getGlobalParameterName(int index) const¶

Get the name of a global parameter.

Parameters: index – the index of the parameter for which to get the name
Returns: the parameter name

void setGlobalParameterName(int index, const std::string &name)¶

Set the name of a global parameter.

Parameters

index – the index of the parameter for which to set the name
name – the name of the parameter

double getGlobalParameterDefaultValue(int index) const¶

Get the default value of a global parameter.

Parameters: index – the index of the parameter for which to get the default value
Returns: the parameter default value

void setGlobalParameterDefaultValue(int index, double defaultValue)¶

Set the default value of a global parameter.

Parameters

index – the index of the parameter for which to set the default value
defaultValue – the default value of the parameter

int addParticleParameterOffset(const std::string &parameter, int particleIndex, double chargeScale, double sigmaScale, double epsilonScale)¶

Add an offset to the per-particle parameters of a particular particle, based on a global parameter.

Parameters

parameter – the name of the global parameter. It must have already been added with addGlobalParameter(). Its value can be modified at any time by calling Context::setParameter().
particleIndex – the index of the particle whose parameters are affected
chargeScale – this value multiplied by the parameter value is added to the particle’s charge
sigmaScale – this value multiplied by the parameter value is added to the particle’s sigma
epsilonScale – this value multiplied by the parameter value is added to the particle’s epsilon

Returns

the index of the offset that was added

void getParticleParameterOffset(int index, std::string &parameter, int &particleIndex, double &chargeScale, double &sigmaScale, double &epsilonScale) const¶

Get the offset added to the per-particle parameters of a particular particle, based on a global parameter.

Parameters

index – the index of the offset to query, as returned by addParticleParameterOffset()
parameter – the name of the global parameter
particleIndex – the index of the particle whose parameters are affected
chargeScale – this value multiplied by the parameter value is added to the particle’s charge
sigmaScale – this value multiplied by the parameter value is added to the particle’s sigma
epsilonScale – this value multiplied by the parameter value is added to the particle’s epsilon

void setParticleParameterOffset(int index, const std::string &parameter, int particleIndex, double chargeScale, double sigmaScale, double epsilonScale)¶

Set the offset added to the per-particle parameters of a particular particle, based on a global parameter.

Parameters

index – the index of the offset to modify, as returned by addParticleParameterOffset()
parameter – the name of the global parameter. It must have already been added with addGlobalParameter(). Its value can be modified at any time by calling Context::setParameter().
particleIndex – the index of the particle whose parameters are affected
chargeScale – this value multiplied by the parameter value is added to the particle’s charge
sigmaScale – this value multiplied by the parameter value is added to the particle’s sigma
epsilonScale – this value multiplied by the parameter value is added to the particle’s epsilon

int addExceptionParameterOffset(const std::string &parameter, int exceptionIndex, double chargeProdScale, double sigmaScale, double epsilonScale)¶

Add an offset to the parameters of a particular exception, based on a global parameter.

Parameters

parameter – the name of the global parameter. It must have already been added with addGlobalParameter(). Its value can be modified at any time by calling Context::setParameter().
exceptionIndex – the index of the exception whose parameters are affected
chargeProdScale – this value multiplied by the parameter value is added to the exception’s charge product
sigmaScale – this value multiplied by the parameter value is added to the exception’s sigma
epsilonScale – this value multiplied by the parameter value is added to the exception’s epsilon

Returns

the index of the offset that was added

void getExceptionParameterOffset(int index, std::string &parameter, int &exceptionIndex, double &chargeProdScale, double &sigmaScale, double &epsilonScale) const¶

Get the offset added to the parameters of a particular exception, based on a global parameter.

Parameters

index – the index of the offset to query, as returned by addExceptionParameterOffset()
parameter – the name of the global parameter
exceptionIndex – the index of the exception whose parameters are affected
chargeProdScale – this value multiplied by the parameter value is added to the exception’s charge product
sigmaScale – this value multiplied by the parameter value is added to the exception’s sigma
epsilonScale – this value multiplied by the parameter value is added to the exception’s epsilon

void setExceptionParameterOffset(int index, const std::string &parameter, int exceptionIndex, double chargeProdScale, double sigmaScale, double epsilonScale)¶

Set the offset added to the parameters of a particular exception, based on a global parameter.

Parameters

index – the index of the offset to modify, as returned by addExceptionParameterOffset()
parameter – the name of the global parameter. It must have already been added with addGlobalParameter(). Its value can be modified at any time by calling Context::setParameter().
exceptionIndex – the index of the exception whose parameters are affected
chargeProdScale – this value multiplied by the parameter value is added to the exception’s charge product
sigmaScale – this value multiplied by the parameter value is added to the exception’s sigma
epsilonScale – this value multiplied by the parameter value is added to the exception’s epsilon

inline bool getUseDispersionCorrection() const¶: Get whether to add a contribution to the energy that approximately represents the effect of Lennard-Jones 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.

inline void setUseDispersionCorrection(bool useCorrection)¶: Set whether to add a contribution to the energy that approximately represents the effect of Lennard-Jones 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.

int getReciprocalSpaceForceGroup() const¶: Get the force group that reciprocal space interactions for Ewald or PME are included in. This allows multiple time step integrators to evaluate direct and reciprocal space interactions at different intervals: getForceGroup() specifies the group for direct space, and getReciprocalSpaceForceGroup() specifies the group for reciprocal space. If this is -1 (the default value), the same force group is used for reciprocal space as for direct space.

void setReciprocalSpaceForceGroup(int group)¶

Set the force group that reciprocal space interactions for Ewald or PME are included in. This allows multiple time step integrators to evaluate direct and reciprocal space interactions at different intervals: setForceGroup() specifies the group for direct space, and setReciprocalSpaceForceGroup() specifies the group for reciprocal space. If this is -1 (the default value), the same force group is used for reciprocal space as for direct space.

Parameters: group – the group index. Legal values are between 0 and 31 (inclusive), or -1 to use the same force group that is specified for direct space.

bool getIncludeDirectSpace() const¶: Get whether to include direct space interactions when calculating forces and energies. This is useful if you want to completely replace the direct space calculation, typically with a CustomNonbondedForce that computes it in a nonstandard way, while still using this object for the reciprocal space calculation.

void setIncludeDirectSpace(bool include)¶: Set whether to include direct space interactions when calculating forces and energies. This is useful if you want to completely replace the direct space calculation, typically with a CustomNonbondedForce that computes it in a nonstandard way, while still using this object for the reciprocal space calculation.

void updateParametersInContext(Context &context)¶

Update the particle and exception 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() and setExceptionParameters() to modify this object’s parameters, then call updateParametersInContext() to copy them over to the Context.

This method has several limitations. The only information it updates is the parameters of particles and exceptions. All other aspects of the Force (the nonbonded method, the cutoff distance, etc.) are unaffected and can only be changed by reinitializing the Context. Furthermore, only the chargeProd, sigma, and epsilon values of an exception can be changed; the pair of particles involved in the exception cannot change. Finally, this method cannot be used to add new particles or exceptions, only to change the parameters of existing ones.

inline virtual bool usesPeriodicBoundaryConditions() const¶

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

Returns: true if force uses PBC and false otherwise

bool getExceptionsUsePeriodicBoundaryConditions() const¶

Get whether periodic boundary conditions should be applied to exceptions. Usually this is not appropriate, because exceptions are normally used to represent bonded interactions (1-2, 1-3, and 1-4 pairs), but there are situations when it does make sense. For example, you may want to simulate an infinite chain where one end of a molecule is bonded to the opposite end of the next periodic copy.

Regardless of this value, periodic boundary conditions are only applied to exceptions if they also are applied to other interactions. If the nonbonded method is NoCutoff or CutoffNonPeriodic, this value is ignored. Also note that cutoffs are never applied to exceptions, again because they are normally used to represent bonded interactions.

void setExceptionsUsePeriodicBoundaryConditions(bool periodic)¶

Set whether periodic boundary conditions should be applied to exceptions. Usually this is not appropriate, because exceptions are normally used to represent bonded interactions (1-2, 1-3, and 1-4 pairs), but there are situations when it does make sense. For example, you may want to simulate an infinite chain where one end of a molecule is bonded to the opposite end of the next periodic copy.

Regardless of this value, periodic boundary conditions are only applied to exceptions if they also get applied to other interactions. If the nonbonded method is NoCutoff or CutoffNonPeriodic, this value is ignored. Also note that cutoffs are never applied to exceptions, again because they are normally used to represent bonded interactions.

NonbondedForce¶

`NonbondedForce`¶