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 callingsetStretchBendParameters()
. This will have no effect on Contexts that already exist unless you callupdateParametersInContext()
.Methods
Create an
AmoebaStretchBendForce
.Get the number of stretch-bend terms in the potential function
Add a stretch-bend term to the force field.
Get the force field parameters for a stretch-bend term.
Set the force field parameters for a stretch-bend term.
Update the per-stretch-bend term parameters in a
Context
to match those stored in thisForce
object.Set whether this force should apply periodic boundary conditions when calculating displacements.
Returns whether or not this force makes use of periodic boundary conditions.
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AmoebaStretchBendForce
()¶ Create an
AmoebaStretchBendForce()
.
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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
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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)
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void
updateParametersInContext
(Context &context)¶ Update the per-stretch-bend term 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 callsetStretchBendParameters()
to modify this object’s parameters, then callupdateParametersInContext()
to copy them over to theContext
.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.
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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.
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bool
usesPeriodicBoundaryConditions
() const¶ Returns whether or not this force makes use of periodic boundary conditions.
- Returns
true if force uses PBC and false otherwise
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