BioSimSpace.Metadynamics.CollectiveVariable.RMSD¶

class BioSimSpace.Metadynamics.CollectiveVariable.RMSD(system, reference, rmsd_indices, reference_index=None, hill_width=0.1000 nm, lower_bound=None, upper_bound=None, grid=None, alignment_type='optimal', pbc=True, property_map={})¶

A class for a root-mean-square deviation (RMSD) collective variable.

__init__(system, reference, rmsd_indices, reference_index=None, hill_width=0.1000 nm, lower_bound=None, upper_bound=None, grid=None, alignment_type='optimal', pbc=True, property_map={})¶

Constructor.

Parameters

system (System) – The molecular system of interest.
reference (Molecule) – The reference molecule, against which the RMSD will be measured. This molecule should match with a single molecule from the system, i.e. contain the same residues as the matching molecule in the same order.
rmsd_indices ([int]) – The indices of the atoms within the reference that should be used when calculating the RMSD. Atoms from the reference that are not in rmsd_indices will instead be used for alignment.
reference_index (int) – The index of the molecule in the system that matches the reference. If none, then we will assume that the molecule with the closest number of residues is the match. If not all atoms from the reference are matched in the system, then an exception will be thrown.
hill_width (Length) – The width of the Gaussian hill used to sample this variable.
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.
alignment_type (str) – The mannier in which RMSD alignment is performed. Options are “optimal” or “simple”.
pbc (bool) – Whether to use periodic boundary conditions when computing the collective variable.
property_map (dict) – A dictionary that maps system “properties” to their user defined values. This allows the user to refer to properties with their own naming scheme, e.g. { “charge” : “my-charge” }

Methods

`__init__`(system, reference, rmsd_indices[, …])	Constructor.
`getAlignmentType`()	Return the RMSD alignment type.
`getGrid`()	Get the grid on which the collective variable is sampled.
`getHillWidth`()	Return the width of the Gaussian hill used to bias this collective variable.
`getInitialValue`()	Return the initial value of the collective variable.
`getLowerBound`()	Get the lower bound on the collective variable.
`getPeriodicBoundaries`()	Return whether to take account of periodic boundary conditions when computing the collective variable.
`getReferenceIndex`()	Return the index of the molecule in the system that corresponds to the reference.
`getReferencePDB`()	Return the reference PDB file as a list of strings.
`getUpperBound`()	Get the upper bound on the collective variable.
`nComponents`()	Return the number of components for the collective variable.
`setAlignmentType`(alignment_type)	Set the RMSD alignment type.
`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.
`setPeriodicBoundaries`(pbc)	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.

getAlignmentType()¶

Return the RMSD alignment type.

Returns: alignment_type – The RMSD alignment type.
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: Grid

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: Length

getInitialValue()¶

Return the initial value of the collective variable.

Returns: rmsd – The initial value of the collective variable.
Return type: Length

getLowerBound()¶

Get the lower bound on the collective variable.

Returns: lower_bound – The lower bound on the value of the collective variable.
Return type: Bound

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

getReferenceIndex()¶

Return the index of the molecule in the system that corresponds to the reference.

Returns

reference_indexint: The index of the molecule in the system that corresponds to the reference.

getReferencePDB()¶

Return the reference PDB file as a list of strings.

Returns: pdb – The reference PDB file as list of strings.
Return type: [str]

getUpperBound()¶

Get the upper bound on the collective variable.

Returns: upper_bound – The upper bound on the value of the collective variable.
Return type: Bound

nComponents()¶: Return the number of components for the collective variable.

setAlignmentType(alignment_type)¶

Set the RMSD alignment type. Options are “optimal” or “simple”.

Parameters: alignment_type (str) – The RMSD alignment type.

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_widthLength: The width of the Gaussian hill.

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.