HarmonicBondForce

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

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().

__init__(self) → HarmonicBondForce

__init__(self, other) -> HarmonicBondForce

Create a HarmonicBondForce.

Methods

__init__((self) -> HarmonicBondForce) __init__(self, other) -> HarmonicBondForce
addBond((self, particle1, particle2, length, ...) Add a bond term to the force field.
getBondParameters(self, index) Get the force field parameters for a bond term.
getForceGroup((self) -> int) Get the force group this Force belongs to.
getNumBonds((self) -> int) Get the number of harmonic bond stretch terms in the potential function
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) -> bool) Returns whether or not this force makes use of periodic boundary conditions.
getNumBonds(self) → int

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

addBond(self, particle1, particle2, length, k) → 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
  • k (double) – the harmonic force constant for the bond, measured in kJ/mol/nm^2
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
  • k (double) – the harmonic force constant for the bond, measured in kJ/mol/nm^2
setBondParameters(self, index, particle1, particle2, length, k)

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
  • k (double) – the harmonic force constant for the bond, measured in kJ/mol/nm^2
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
__delattr__

x.__delattr__(‘name’) <==> del x.name

__format__()

default object formatter

__getattribute__

x.__getattribute__(‘name’) <==> x.name

__hash__
__reduce__()

helper for pickle

__reduce_ex__()

helper for pickle

__sizeof__() → int

size of object in memory, in bytes

__str__
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).