BioSimSpace.Metadynamics.CollectiveVariable.RMSD

class BioSimSpace.Metadynamics.CollectiveVariable.RMSD(system, reference, align_selection, rmsd_selection, reference_mapping=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, align_selection, rmsd_selection, reference_mapping=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 (System) – The reference system, against which the RMSD will be measured.

• align_selection (str) – A Sire selection string that defines the atoms to be used when aligning the two structures. If None, then the RMSD will be calculated without alignment.

• rmsd_selection (str) – A Sire selection string that defines the atoms to be used when calculating the RMSD.

• reference_mapping (dict) – A dictionary mapping molecule indices in the reference to those in the system. This must be used when the reference represents a sub-set of the system.

• 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, align_selection, ...)	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.
getMoleculeIndices()	Return the indices of molecules involved in the collective variable.
getPeriodicBoundaries()	Return whether to take account of periodic boundary conditions when computing the collective variable.
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

getMoleculeIndices()

Return the indices of molecules involved in the collective variable.

Returns:

molecule_indices – The indices of molecules involved in the collective variable.

Return type:

int

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

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.