BioSimSpace.Metadynamics.CollectiveVariable.Funnel¶
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class
BioSimSpace.Metadynamics.CollectiveVariable.Funnel(atoms0, atoms1, hill_width=(0.0250 nm, 0.0500 nm), width=0.6000 nm, buffer=0.1500 nm, steepness=1.5, inflection=2.0000 nm, lower_bound=<BioSimSpace.Metadynamics.Bound: value=0.5000 nm, force_constant=2000.0, exponent=2.0, epsilon=1.0>, upper_bound=<BioSimSpace.Metadynamics.Bound: value=4.0000 nm, force_constant=2000.0, exponent=2.0, epsilon=1.0>, grid=(<BioSimSpace.Metadynamics.Grid: minimum=0.0000e+00 nm, maximum=4.5000 nm, num_bins=400>, <BioSimSpace.Metadynamics.Grid: minimum=0.0000e+00 nm, maximum=0.9000 nm, num_bins=400>))¶ A class for a funnel collective variable.
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__init__(atoms0, atoms1, hill_width=(0.0250 nm, 0.0500 nm), width=0.6000 nm, buffer=0.1500 nm, steepness=1.5, inflection=2.0000 nm, lower_bound=<BioSimSpace.Metadynamics.Bound: value=0.5000 nm, force_constant=2000.0, exponent=2.0, epsilon=1.0>, upper_bound=<BioSimSpace.Metadynamics.Bound: value=4.0000 nm, force_constant=2000.0, exponent=2.0, epsilon=1.0>, grid=(<BioSimSpace.Metadynamics.Grid: minimum=0.0000e+00 nm, maximum=4.5000 nm, num_bins=400>, <BioSimSpace.Metadynamics.Grid: minimum=0.0000e+00 nm, maximum=0.9000 nm, num_bins=400>))¶ Constructor.
- Parameters
atoms0 ([int, int, ..]) – A list of atom indices that define the origin of the funnel.
atoms1 ([int, int, ..]) – A list of atom indices that define the inflection point of the funnel.
width (
Length) – The funnel “wall width”.buffer (
Length) – The funnel “wall buffer”.steepness (float) – The steepness of the funnel at the inflection point.
inflection (
Length) – The inflection point as a value of the projection along the funnel axis.hill_width ((
Length, “class:Length)) – The width of the Gaussian hill used to sample each component of the collective variable.lower_bound (
Bound) – A lower bound on the value of the collective variable. This is used to constrain the “projection on axis” component of the collective variable, i.e. the distance from the funnel axis to the origin, along the axis.upper_bound (
Bound) – An upper bound on the value of the collective variable. This is used to constrain the “projection on axis” component of the collective variable, i.e. the distance from the funnel axis to the origin, along the axis.grid ((
Grid,Grid)) – The grid on which the collective variable will be sampled. This can help speed up long metadynamics simulations where the number of Gaussian kernels can become prohibitive. The collective variable has two components: the “projection on the funnel axis” (the distance from the axis to the origin, along the axis) and the orthogonal distance between the ligand and the axis. The grid should be passed as a tuple with the parameters for each component.
Methods
__init__(atoms0, atoms1[, hill_width, …])Constructor.
Return indices of the atoms whose center-of-mass defines the origin of the funnel.
Return indices of the atoms whose center-of-mass defines the inflection point of the funnel.
Return the funnel “wall buffer”.
getCorrection([proj_min, proj_max, delta])Get the funnel correction term.
getExtent(projection)Return a value of the funnel extent for a given distance along the projection axis.
getGrid()Get the grid on which the collective variable is sampled.
Return the width of the Gaussian hill used to bias this collective variable.
Return the inflection point as a value of the projection along the funnel axis.
Get the lower bound on the collective variable.
Return the steepness of the funnel at the inflection point.
Get the upper bound on the collective variable.
getWidth()Return the funnel “wall width”.
Return the number of components for the collective variable.
setAtoms0(atoms0)Set the list of atom indices whose center-of-mass define the origin of the funnel.
setAtoms1(atoms1)Set the list of atom indices whose center-of-mass define the inflection point of the funnel.
setBuffer(buffer)Set the funnel “wall buffer”.
setGrid([grid])Set a grid on which the collective variable will be sampled.
setHillWidth(hill_width)Set the width of the Gaussian hills used to bias this collective variable.
setInflection(inflection)Set the inflection point as a value of the projection along the funnel axis.
setLowerBound([lower_bound])Set a lower bound on the value of the collective variable.
setSteepness(steepness)Set the steepness of the funnel at the inflection point.
setUpperBound([upper_bound])Set an upper bound on the value of the collective variable.
setWidth(width)Set the funnel “wall width”.
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getAtoms0()¶ Return indices of the atoms whose center-of-mass defines the origin of the funnel.
- Returns
atoms0 – The list of atom indices whose center-of-mass define the origin of the funnel.
- Return type
[int]
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getAtoms1()¶ Return indices of the atoms whose center-of-mass defines the inflection point of the funnel.
- Returns
atoms1 – The list of atom indices whose center-of-mass define the inflection point of the funnel.
- Return type
[int]
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getBuffer()¶ Return the funnel “wall buffer”.
- Returns
buffer – The funnel “wall buffer”.
- Return type
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getCorrection(proj_min=None, proj_max=None, delta=0.0100 nm)¶ Get the funnel correction term. This is the correction factor for free-energy estimates that takes into account the reduction in entropy caused by the funnel restraint.
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getExtent(projection)¶ Return a value of the funnel extent for a given distance along the projection axis.
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getGrid()¶ Get the grid on which the collective variable is sampled.
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getHillWidth()¶ Return the width of the Gaussian hill used to bias this collective variable.
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getInflection()¶ Return the inflection point as a value of the projection along the funnel axis.
- Returns
inflection – The inflection point as avalue of the projection along the funnel axis.
- Return type
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getLowerBound()¶ Get the lower bound on the collective variable.
- Returns
lower_bound – The lower bound on the value of the collective variable.
- Return type
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getSteepness()¶ Return the steepness of the funnel at the inflection point.
- Returns
steepness – The steepness of the funnel at the inflection point.
- Return type
float
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getUpperBound()¶ Get the upper bound on the collective variable.
- Returns
upper_bound – The upper bound on the value of the collective variable.
- Return type
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getWidth()¶ Return the funnel “wall width”.
- Returns
width – The funnel “wall width”.
- Return type
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nComponents()¶ Return the number of components for the collective variable.
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setAtoms0(atoms0)¶ Set the list of atom indices whose center-of-mass define the origin of the funnel.
- Parameters
atoms0 ([int, int, ..]) – The list of atom indices whose center-of-mass define the origin of the funnel.
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setAtoms1(atoms1)¶ Set the list of atom indices whose center-of-mass define the inflection point of the funnel.
- Parameters
atoms1 ([int, int, ..]) – The list of atom indices whose center-of-mass define the inflection point of the funnel.
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setBuffer(buffer)¶ Set the funnel “wall buffer”.
- Parameters
buffer (
Length) – The width of the funnel wall buffer.
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setGrid(grid=None)¶ Set a grid on which the collective variable will be sampled. Call with no arguments to clear the grid.
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setHillWidth(hill_width)¶ Set the width of the Gaussian hills used to bias this collective variable.
- Parameters
hill_width (
Length) – The width of the Gaussian hill for the two components of the collective variable: the distance along the funnel projection axis, and the orthogonal extent from the axis.
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setInflection(inflection)¶ Set the inflection point as a value of the projection along the funnel axis.
- Parameters
inflection (
Length) – The inflection point as avalue of the projection along the funnel axis.
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setLowerBound(lower_bound=None)¶ Set a lower bound on the value of the collective variable.
- Parameters
lower_bound (
Bound) – A lower bound on the value of the collective variable.
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setSteepness(steepness)¶ Set the steepness of the funnel at the inflection point.
- Parameters
steepness (float) – The steepness of the funnel at the inflection point.
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