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 perbond. The coefficients of the higher order terms each have a single value that is set globally.
To use it, create an
AmoebaBondForce
object then calladdBond()
once for each bond. After a bond has been added, you can modify its force field parameters by callingsetBondParameters()
. This will have no effect on Contexts that already exist unless you callupdateParametersInContext()
.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 perbond parameters in a Context
to match those stored in thisForce
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 perbond 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 callsetBondParameters()
to modify this object’s parameters, then callupdateParametersInContext()
to copy them over to theContext
.The only information this method updates is the values of perbond 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
