AmoebaBondForce

class simtk.openmm.openmm.AmoebaBondForce(*args)

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().

__init__(self) → AmoebaBondForce

__init__(self, other) -> AmoebaBondForce

Create an AmoebaBondForce.

Methods

__init__(self) __init__(self, other) -> AmoebaBondForce
addBond(self, particle1, particle2, length, …) Add a bond term to the force field.
getAmoebaGlobalBondCubic(self) Get the global cubic term
getAmoebaGlobalBondQuartic(self) Get the global quartic term
getBondParameters(self, index) Get the force field parameters for a bond term.
getForceGroup(self) Get the force group this Force belongs to.
getNumBonds(self) Get the number of bond stretch terms in the potential function
setAmoebaGlobalBondCubic(self, cubicK) Set the global cubic term
setAmoebaGlobalBondQuartic(self, quarticK) Set the global quartic term
setBondParameters(self, index, particle1, …) Set the force field parameters for a bond term.
setForceGroup(self, group) Set the force group this Force belongs to.
setUsesPeriodicBoundaryConditions(self, periodic) Set whether this force should apply periodic boundary conditions when calculating displacements.
updateParametersInContext(self, context) Update the per-bond parameters in a Context to match those stored in this Force object.
usesPeriodicBoundaryConditions(self) Returns whether or not this force makes use of periodic boundary conditions.
getNumBonds(self) → int

Get the number of bond stretch terms in the potential function

setAmoebaGlobalBondCubic(self, cubicK)

Set the global cubic term

Parameters:cubicK (double) – the cubic force constant for the bond
getAmoebaGlobalBondCubic(self) → double

Get the global cubic term

Returns:global cubicK term
Return type:double
setAmoebaGlobalBondQuartic(self, quarticK)

Set the global quartic term

Parameters:quarticK (double) – the quartic force constant for the bond
getAmoebaGlobalBondQuartic(self) → double

Get the global quartic term

Returns:global quartic term
Return type:double
addBond(self, particle1, particle2, length, quadraticK) → int

Add a bond term to the force field.

Parameters:
  • particle1 (int) – the index of the first particle connected by the bond
  • particle2 (int) – the index of the second particle connected by the bond
  • length (double) – the equilibrium length of the bond, measured in nm
  • quadraticK (double) – the quadratic force constant for the bond
Returns:

the index of the bond that was added
Return type:

int
getBondParameters(self, index)

Get the force field parameters for a bond term.

Parameters:index (int) – the index of the bond for which to get parameters
Returns:
  • particle1 (int) – the index of the first particle connected by the bond
  • particle2 (int) – the index of the second particle connected by the bond
  • length (double) – the equilibrium length of the bond, measured in nm
  • quadraticK (double) – the quadratic force constant for the bond
setBondParameters(self, index, particle1, particle2, length, quadraticK)

Set the force field parameters for a bond term.

Parameters:
  • index (int) – the index of the bond for which to set parameters
  • particle1 (int) – the index of the first particle connected by the bond
  • particle2 (int) – the index of the second particle connected by the bond
  • length (double) – the equilibrium length of the bond, measured in nm
  • quadraticK (double) – the quadratic force constant for the bond
updateParametersInContext(self, 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.

setUsesPeriodicBoundaryConditions(self, 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.

usesPeriodicBoundaryConditions(self) → bool

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

Returns:true if force uses PBC and false otherwise
Return type:bool
__copy__(self) → Force
getForceGroup(self) → int

Get the force group this Force belongs to.

setForceGroup(self, group)

Set the force group this Force belongs to.

Parameters:group (int) – the group index. Legal values are between 0 and 31 (inclusive).