AmoebaBondForce

class OpenMM::AmoebaBondForce

This class implements an interaction between pairs of particles that varies with the distance between them. The interaction is defined by a 4th order polynomial. Only the quadratic term is set per-bond. The coefficients of the higher order terms each have a single value that is set globally.

To use it, create an AmoebaBondForce 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

AmoebaBondForce

Create an AmoebaBondForce.

getNumBonds

Get the number of bond stretch terms in the potential function

setAmoebaGlobalBondCubic

Set the global cubic term

getAmoebaGlobalBondCubic

Get the global cubic term

setAmoebaGlobalBondQuartic

Set the global quartic term

getAmoebaGlobalBondQuartic

Get the global quartic term

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.
AmoebaBondForce()

Create an AmoebaBondForce().

int getNumBonds() const

Get the number of bond stretch terms in the potential function

void setAmoebaGlobalBondCubic(double cubicK)

Set the global cubic term

Parameters

  • cubicK – the cubic force constant for the bond

double getAmoebaGlobalBondCubic() const

Get the global cubic term

Returns

global cubicK term

void setAmoebaGlobalBondQuartic(double quarticK)

Set the global quartic term

Parameters

  • quarticK – the quartic force constant for the bond

double getAmoebaGlobalBondQuartic() const

Get the global quartic term

Returns

global quartic term

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

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

  • quadraticK – the quadratic force constant for the bond

Returns

the index of the bond that was added

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

  • quadraticK – [out] the quadratic force constant for the bond

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

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

  • quadraticK – the quadratic force constant for the bond

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