AmoebaStretchBendForce

class OpenMM::AmoebaStretchBendForce

This class implements the Amoeba stretch-bend interaction.

To use it, create a StretchBendForce object then call addStretchBend() once for each stretch-bend. After a stretch-bend has been added, you can modify its force field parameters by calling setStretchBendParameters(). This will have no effect on Contexts that already exist unless you call updateParametersInContext().

Methods

AmoebaStretchBendForce Create an AmoebaStretchBendForce.
getNumStretchBends Get the number of stretch-bend terms in the potential function
addStretchBend Add a stretch-bend term to the force field.
getStretchBendParameters Get the force field parameters for a stretch-bend term.
setStretchBendParameters Set the force field parameters for a stretch-bend term.
updateParametersInContext Update the per-stretch-bend term 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.
AmoebaStretchBendForce()

Create an AmoebaStretchBendForce().

int getNumStretchBends() const

Get the number of stretch-bend terms in the potential function

int addStretchBend(int particle1, int particle2, int particle3, double lengthAB, double lengthCB, double angle, double k1, double k2)

Add a stretch-bend term to the force field.

Parameters:
  • particle1 – the index of the first particle connected by the stretch-bend
  • particle2 – the index of the second particle connected by the stretch-bend
  • particle3 – the index of the third particle connected by the stretch-bend
  • lengthAB – the equilibrium length of the stretch-bend in bond ab [particle1, particle2], measured in nm
  • lengthCB – the equilibrium length of the stretch-bend in bond cb [particle3, particle2], measured in nm
  • angle – the equilibrium angle in radians
  • k1 – the force constant of the product of bond ab and angle a-b-c
  • k2 – the force constant of the product of bond bc and angle a-b-c (optional, default is the same as k1)
Returns:the index of the stretch-bend that was added
void getStretchBendParameters(int index, int &particle1, int &particle2, int &particle3, double &lengthAB, double &lengthCB, double &angle, double &k1, double &k2) const

Get the force field parameters for a stretch-bend term.

Parameters:
  • index – the index of the stretch-bend for which to get parameters
  • particle1 – [out] the index of the first particle connected by the stretch-bend
  • particle2 – [out] the index of the second particle connected by the stretch-bend
  • particle3 – [out] the index of the third particle connected by the stretch-bend
  • lengthAB – [out] the equilibrium length of the stretch-bend in bond ab [particle1, particle2], measured in nm
  • lengthCB – [out] the equilibrium length of the stretch-bend in bond cb [particle3, particle2], measured in nm
  • angle – [out] the equilibrium angle in radians
  • k1 – [out] the force constant of the product of bond ab and angle a-b-c
  • k2 – [out] the force constant of the product of bond bc and angle a-b-c
void setStretchBendParameters(int index, int particle1, int particle2, int particle3, double lengthAB, double lengthCB, double angle, double k1, double k2)

Set the force field parameters for a stretch-bend term.

Parameters:
  • index – the index of the stretch-bend for which to set parameters
  • particle1 – the index of the first particle connected by the stretch-bend
  • particle2 – the index of the second particle connected by the stretch-bend
  • particle3 – the index of the third particle connected by the stretch-bend
  • lengthAB – the equilibrium length of the stretch-bend in bond ab [particle1, particle2], measured in nm
  • lengthCB – the equilibrium length of the stretch-bend in bond cb [particle3, particle2], measured in nm
  • angle – the equilibrium angle in radians
  • k1 – the force constant of the product of bond ab and angle a-b-c
  • k2 – the force constant of the product of bond bc and angle a-b-c (optional, default is the same as k1)
void updateParametersInContext(Context &context)

Update the per-stretch-bend term 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 setStretchBendParameters() 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-stretch-bend term parameters. The set of particles involved in a term cannot be changed, nor can new terms 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