HarmonicBondForce

class OpenMM::HarmonicBondForce

This class implements an interaction between pairs of particles that varies harmonically with the distance between them. To use it, create a HarmonicBondForce object then call addBond() once for each bond. After a bond has been added, you can modify its force field parameters by calling setBondParameters(). This will have no effect on Contexts that already exist unless you call updateParametersInContext().

Methods

HarmonicBondForce	Create a HarmonicBondForce.
getNumBonds	Get the number of harmonic bond stretch terms in the potential function
addBond	Add a bond term to the force field.
getBondParameters	Get the force field parameters for a bond term.
setBondParameters	Set the force field parameters for a bond term.
updateParametersInContext	Update the per-bond parameters in a Context to match those stored in this Force object.
setUsesPeriodicBoundaryConditions	Set whether this force should apply periodic boundary conditions when calculating displacements.
usesPeriodicBoundaryConditions	Returns whether or not this force makes use of periodic boundary conditions.

HarmonicBondForce()

Create a HarmonicBondForce().

int getNumBonds() const

Get the number of harmonic bond stretch terms in the potential function

int addBond(int particle1, int particle2, double length, double k)

Add a bond term to the force field.

Parameters:

• particle1 – the index of the first particle connected by the bond
• particle2 – the index of the second particle connected by the bond
• length – the equilibrium length of the bond, measured in nm
• k – the harmonic force constant for the bond, measured in kJ/mol/nm^2

Returns:the index of the bond that was added

void getBondParameters(int index, int &particle1, int &particle2, double &length, double &k) const

Get the force field parameters for a bond term.

Parameters:

• index – the index of the bond for which to get parameters
• particle1 – [out] the index of the first particle connected by the bond
• particle2 – [out] the index of the second particle connected by the bond
• length – [out] the equilibrium length of the bond, measured in nm
• k – [out] the harmonic force constant for the bond, measured in kJ/mol/nm^2

void setBondParameters(int index, int particle1, int particle2, double length, double k)

Set the force field parameters for a bond term.

Parameters:

• index – the index of the bond for which to set parameters
• particle1 – the index of the first particle connected by the bond
• particle2 – the index of the second particle connected by the bond
• length – the equilibrium length of the bond, measured in nm
• k – the harmonic force constant for the bond, measured in kJ/mol/nm^2

void updateParametersInContext(Context &context)

Update the per-bond 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 setBondParameters() 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-bond parameters. The set of particles involved in a bond cannot be changed, nor can new bonds be added.

void setUsesPeriodicBoundaryConditions(bool periodic)

Set whether this force should apply periodic boundary conditions when calculating displacements. Usually this is not appropriate for bonded forces, but there are situations when it can be useful.

bool usesPeriodicBoundaryConditions() const

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

Returns:true if force uses PBC and false otherwise