AmoebaOutOfPlaneBendForce¶
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class
simtk.openmm.openmm.
AmoebaOutOfPlaneBendForce
(*args)¶ This class implements the Amoeba out-of-plane bend interaction.
To use it, create an OutOfPlaneBendForce object then call addOutOfPlaneBend() once for each outOfPlaneBend. After an out-of-plane bend has been added, you can modify its force field parameters by calling setOutOfPlaneBendParameters(). This will have no effect on Contexts that already exist unless you call updateParametersInContext().
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__init__
(self) → AmoebaOutOfPlaneBendForce¶ __init__(self, other) -> AmoebaOutOfPlaneBendForce
Create an AmoebaOutOfPlaneBendForce.
Methods
__init__
((self) -> AmoebaOutOfPlaneBendForce)__init__(self, other) -> AmoebaOutOfPlaneBendForce addOutOfPlaneBend
((self, particle1, ...)Add an out-of-plane bend term to the force field. getAmoebaGlobalOutOfPlaneBendCubic
(...)Get the global cubic term getAmoebaGlobalOutOfPlaneBendPentic
(...)Get the global pentic term getAmoebaGlobalOutOfPlaneBendQuartic
(...)Get the global quartic term getAmoebaGlobalOutOfPlaneBendSextic
(...)Get the global sextic term getForceGroup
((self) -> int)Get the force group this Force belongs to. getNumOutOfPlaneBends
((self) -> int)Get the number of out-of-plane bend terms in the potential function getOutOfPlaneBendParameters
(self, index)Get the force field parameters for an out-of-plane bend term. setAmoebaGlobalOutOfPlaneBendCubic
(self, cubicK)Set the global cubic term setAmoebaGlobalOutOfPlaneBendPentic
(self, ...)Set the global pentic term setAmoebaGlobalOutOfPlaneBendQuartic
(self, ...)Set the global cubic term setAmoebaGlobalOutOfPlaneBendSextic
(self, ...)Set the global sextic term setForceGroup
(self, group)Set the force group this Force belongs to. setOutOfPlaneBendParameters
(self, index, ...)Set the force field parameters for an out-of-plane bend term. setUsesPeriodicBoundaryConditions
(self, periodic)Set whether this force should apply periodic boundary conditions when calculating displacements. updateParametersInContext
(self, context)Update the per-bend term 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. -
getNumOutOfPlaneBends
(self) → int¶ Get the number of out-of-plane bend terms in the potential function
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setAmoebaGlobalOutOfPlaneBendCubic
(self, cubicK)¶ Set the global cubic term
Parameters: cubicK (double) – the cubic force constant for the angle
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getAmoebaGlobalOutOfPlaneBendCubic
(self) → double¶ Get the global cubic term
Returns: global cubicK term Return type: double
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setAmoebaGlobalOutOfPlaneBendQuartic
(self, quarticK)¶ Set the global cubic term
Parameters: quarticK (double) – the quartic force constant for the angle
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getAmoebaGlobalOutOfPlaneBendQuartic
(self) → double¶ Get the global quartic term
Returns: global quartic term Return type: double
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setAmoebaGlobalOutOfPlaneBendPentic
(self, penticK)¶ Set the global pentic term
Parameters: penticK (double) – the pentic force constant for the angle
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getAmoebaGlobalOutOfPlaneBendPentic
(self) → double¶ Get the global pentic term
Returns: global penticK term Return type: double
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setAmoebaGlobalOutOfPlaneBendSextic
(self, sexticK)¶ Set the global sextic term
Parameters: sexticK (double) – the sextic force constant for the angle
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getAmoebaGlobalOutOfPlaneBendSextic
(self) → double¶ Get the global sextic term
Returns: global sexticK term Return type: double
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addOutOfPlaneBend
(self, particle1, particle2, particle3, particle4, k) → int¶ Add an out-of-plane bend term to the force field.
Parameters: - particle1 (int) – the index of the first particle connected by the outOfPlaneBend
- particle2 (int) – the index of the second particle connected by the outOfPlaneBend
- particle3 (int) – the index of the third particle connected by the outOfPlaneBend
- particle4 (int) – the index of the fourth particle connected by the outOfPlaneBend
- k (double) – the force constant for the out-of-plane bend
Returns: the index of the out-of-plane bend that was added
Return type: int
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getOutOfPlaneBendParameters
(self, index)¶ Get the force field parameters for an out-of-plane bend term.
Parameters: index (int) – the index of the outOfPlaneBend for which to get parameters Returns: - particle1 (int) – the index of the first particle connected by the outOfPlaneBend
- particle2 (int) – the index of the second particle connected by the outOfPlaneBend
- particle3 (int) – the index of the third particle connected by the outOfPlaneBend
- particle4 (int) – the index of the fourth particle connected by the outOfPlaneBend
- k (double) – the force constant for the out-of-plane bend
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setOutOfPlaneBendParameters
(self, index, particle1, particle2, particle3, particle4, k)¶ Set the force field parameters for an out-of-plane bend term.
Parameters: - index (int) – the index of the outOfPlaneBend for which to set parameters
- particle1 (int) – the index of the first particle connected by the outOfPlaneBend
- particle2 (int) – the index of the second particle connected by the outOfPlaneBend
- particle3 (int) – the index of the third particle connected by the outOfPlaneBend
- particle4 (int) – the index of the fourth particle connected by the outOfPlaneBend
- k (double) – the force constant for the out-of-plane bend
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updateParametersInContext
(self, context)¶ Update the per-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 setOutOfPlaneBendParameters() 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-bend term parameters. The set of particles involved in a term cannot be changed, nor can new terms be added.
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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.
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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
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__copy__
(self) → Force¶
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getForceGroup
(self) → int¶ Get the force group this Force belongs to.
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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).
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