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Update k_soft docstring. [ci skip]
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Lines changed: 16 additions & 3 deletions

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src/ghostly/_ghostly.py

Lines changed: 16 additions & 3 deletions
Original file line numberDiff line numberDiff line change
@@ -72,7 +72,14 @@ def modify(
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k_soft : float, optional
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The force constant to use when setting angle terms involving ghost atoms
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for non-planar triple junctions. (In kcal/mol/rad^2)
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for non-planar triple junctions. Should be small relative to the
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physical angle force constants of the force field in use, so as not to
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distort the physical end-state geometry, while still providing enough
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anchoring to prevent flapping. Boresch et al. (JCTC 2021) used 3.55
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kcal/mol/rad^2, derived from CGenFF ammonia H-N-H parameters. For
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GAFF (~41 kcal/mol/rad^2) and OpenFF (~54 kcal/mol/rad^2), the default
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of 5 kcal/mol/rad^2 is similarly small relative to the physical force
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constants and is well justified. (In kcal/mol/rad^2)
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optimise_angles : bool, optional
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Whether to optimise the equilibrium value of the angle terms involving
@@ -1167,7 +1174,10 @@ def _triple(
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k_soft : float, optional
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The force constant to use when setting angle terms involving ghost
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atoms for non-planar triple junctions. (In kcal/mol/rad^2)
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atoms for non-planar triple junctions. Should be small relative to
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the physical angle force constants of the force field in use. For
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GAFF (~41 kcal/mol/rad^2) and OpenFF (~54 kcal/mol/rad^2), the
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default of 5 kcal/mol/rad^2 is appropriate. (In kcal/mol/rad^2)
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optimise_angles : bool, optional
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Whether to optimise the equilibrium value of the angle terms involving
@@ -1636,7 +1646,10 @@ def _higher(
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k_soft : float, optional
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The force constant to use when setting angle terms involving ghost
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atoms for non-planar triple junctions. (In kcal/mol/rad^2)
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atoms for non-planar triple junctions. Should be small relative to
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the physical angle force constants of the force field in use. For
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GAFF (~41 kcal/mol/rad^2) and OpenFF (~54 kcal/mol/rad^2), the
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default of 5 kcal/mol/rad^2 is appropriate. (In kcal/mol/rad^2)
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optimise_angles : bool, optional
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Whether to optimise the equilibrium value of the angle terms involving

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