BioSimSpace.Metadynamics.CollectiveVariable.Distance¶
-
class
BioSimSpace.Metadynamics.CollectiveVariable.
Distance
(atom0, atom1, hill_width=0.1000 nm, weights0=None, weights1=None, is_com0=None, is_com1=None, lower_bound=None, upper_bound=None, grid=None, component=None, pbc=True)¶ A class for distance based collective variables.
-
__init__
(atom0, atom1, hill_width=0.1000 nm, weights0=None, weights1=None, is_com0=None, is_com1=None, lower_bound=None, upper_bound=None, grid=None, component=None, pbc=True)¶ Constructor.
- Parameters
atom0 (int, [int, int, …],
Coordinate
) – The atom, group of atoms, or coordinate, that the distance will be measured from.atom1 (int, [int, int, …],
Coordinate
) – The atom, group of atoms, or coordinate, that the distance will be measured to.hill_width (
Length
) – The width of the Gaussian hill used to sample this variable.weights0 ([float]) – A list of weights to be used when computing the center of the first atom group. This is ignored when a single index is passed for ‘atom0’.
weights1 ([float]) – A list of weights to be used when computing the center of the second atom group. This is ignored when a single index is passed for ‘atom1’.
is_com0 (bool) – Whether to compute the center of mass of the first atom group. If True, this option will take precedence over any weights passed in via ‘weights0’.
is_com1 (bool) – Whether to compute the center of mass of the second atom group. If True, this option will take precedence over any weights passed in via ‘weights1’.
lower_bound (
Bound
) – A lower bound on the value of the collective variable.upper_bound (
Bound
) – An upper bound on the value of the collective variable.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.component (str) – Whether to use the ‘x’, ‘y’, or ‘z’ component of the distance as the collective variable. If None, then the full Euclidean distance is used.
pbc (bool) – Whether to use periodic boundary conditions when computing the collective variable.
Methods
__init__
(atom0, atom1[, hill_width, …])Constructor.
getAtom0
()Return the atom, atoms, or coordinate, that the distance will be measured from.
getAtom1
()Return the atom, atoms, or coordinate, that the distance will be measured to.
getCoM0
()Whether to compute the center of mass of the first atom group.
getCoM1
()Whether to compute the center of mass of the first second group.
Whether to use the ‘x’, ‘y’, or ‘z’ component of the distance as the collective variable.
getGrid
()Get the grid on which the collective variable is sampled.
Return the width of the Gaussian hill used to bias this collective variable.
Get the lower bound on the collective variable.
Return whether to take account of periodic boundary conditions when computing the collective variable.
Get the upper bound on the collective variable.
Get the weights to be used when computing the center of the first atom group.
Get the weights to be used when computing the center of the second atom group.
Return the number of components for the collective variable.
setAtom0
(atom0)Set the atom, atoms, or coordinate from which the distance will be measured.
setAtom1
(atom1)Set the atom, atoms, or coordinate to which the distance will be measured.
setCoM0
([is_com])Set whether to compute the center of mass of the first atom group.
setCoM1
([is_com])Set whether to compute the center of mass of the second atom group.
setComponent
([component])Whether to use the ‘x’, ‘y’, or ‘z’ component of the distance as the collective variable.
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.
setLowerBound
([lower_bound])Set a lower bound on the value of the collective variable.
Set whether to use periodic_boundaries when calculating the collective variable.
setUpperBound
([upper_bound])Set an upper bound on the value of the collective variable.
setWeights0
([weights0])Set the weights to be used when computing the center of the first atom group.
setWeights1
([weights1])Set the weights to be used when computing the center of the second atom group.
-
getAtom0
()¶ Return the atom, atoms, or coordinate, that the distance will be measured from.
- Returns
atom0 – The atom, group of atoms, or coordinate, that the distance will be measured from.
- Return type
int, [int, int, …], [
Length
]
-
getAtom1
()¶ Return the atom, atoms, or coordinate, that the distance will be measured to.
- Returns
atom1 – The atom, group of atoms, or coordinate, that the distance will be measured to.
- Return type
int, [int, int, …], [
Length
]
-
getCoM0
()¶ Whether to compute the center of mass of the first atom group. If True, this option will take precedence over any weights that may have been set.
- Returns
is_com0 – Whether to compute the center of mass of the first atom group.
- Return type
bool
-
getCoM1
()¶ Whether to compute the center of mass of the first second group. If True, this option will take precedence over any weights that may have been set.
- Returns
is_com1 – Whether to compute the center of mass of the first atom group.
- Return type
bool
-
getComponent
()¶ Whether to use the ‘x’, ‘y’, or ‘z’ component of the distance as the collective variable. If unset, then the full Euclidean distance is used.
- Returns
component – ‘x’, ‘y’, or ‘z’
- Return type
str
-
getGrid
()¶ Get the grid on which the collective variable is sampled.
- Returns
grid – The grid on which the collective variable is sampled.
- Return type
-
getHillWidth
()¶ Return the width of the Gaussian hill used to bias this collective variable.
- Returns
hill_width – The width of the Gaussian hill.
- Return type
-
getLowerBound
()¶ Get the lower bound on the collective variable.
- Returns
lower_bound – The lower bound on the value of the collective variable.
- Return type
-
getPeriodicBoundaries
()¶ Return whether to take account of periodic boundary conditions when computing the collective variable.
- Returns
pbc – Whether to use periodic boundaries conditions.
- Return type
bool
-
getUpperBound
()¶ Get the upper bound on the collective variable.
- Returns
upper_bound – The upper bound on the value of the collective variable.
- Return type
-
getWeights0
()¶ Get the weights to be used when computing the center of the first atom group.
- Returns
weights0 – A list of weights to be used when computing the center of the first atom group.
- Return type
[float]
-
getWeights1
()¶ Get the weights to be used when computing the center of the second atom group.
- Returns
weights1 – A list of weights to be used when computing the center of the second atom group.
- Return type
[float]
-
nComponents
()¶ Return the number of components for the collective variable.
-
setAtom0
(atom0)¶ Set the atom, atoms, or coordinate from which the distance will be measured.
- Parameters
atom0 (int, [int, int, …], [
Length
]) – The atom, group of atoms, or coordinate, that the distance will be measured from.
-
setAtom1
(atom1)¶ Set the atom, atoms, or coordinate to which the distance will be measured.
- Parameters
atom1 (int, [int, int, …], [
Length
]) – The atom, group of atoms, or coordinate, that the distance will be measured to.
-
setCoM0
(is_com=None)¶ Set whether to compute the center of mass of the first atom group. If True, this option will take precedence over any weights that may have been set. Can be called with no arguments to clear the data.
- Parameters
is_com (bool) – Whether to compute the center of mass of each atom group.
-
setCoM1
(is_com=None)¶ Set whether to compute the center of mass of the second atom group. If True, this option will take precedence over any weights that may have been set. Can be called with no arguments to clear the data.
- Parameters
is_com (bool) – Whether to compute the center of mass of each atom group.
-
setComponent
(component=None)¶ Whether to use the ‘x’, ‘y’, or ‘z’ component of the distance as the collective variable. If unset, then the full Euclidean distance is used. Can be called with no argument to clear the data.
- Parameters
component (str) – ‘x’, ‘y’, or ‘z’
-
setGrid
(grid=None)¶ Set a grid on which the collective variable will be sampled. Call with no arguments to clear the grid.
- Parameters
grid (
Grid
) – A grid for the collective variable.
-
setHillWidth
(hill_width)¶ Set the width of the Gaussian hills used to bias this collective variable.
- hill_width
Length
The width of the Gaussian hill.
- hill_width
-
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.
-
setPeriodicBoundaries
(pbc)¶ Set whether to use periodic_boundaries when calculating the collective variable.
- Parameters
pbc (bool) – Whether to use periodic boundaries conditions.
-
setUpperBound
(upper_bound=None)¶ Set an upper bound on the value of the collective variable.
- Parameters
upper_bound (
Bound
) – An upper bound on the value of the collective variable.
-
setWeights0
(weights0=None)¶ Set the weights to be used when computing the center of the first atom group. Can be called with no arguments to clear the weights.
- Parameters
weights0 ([float]) – A list of weights to be used when computing the center of the first atom group.
-
setWeights1
(weights1=None)¶ Set the weights to be used when computing the center of the second atom group. Can be called with no arguments to clear the weights.
- Parameters
weights1 ([float]) – A list of weights to be used when computing the center of the second atom group.
-