4.8.2. Linear Density — MDAnalysis.analysis.lineardensity

A tool to compute mass and charge density profiles along the three cartesian axes of the simulation cell. Works only for orthorombic, fixed volume cells (thus for simulations in canonical NVT ensemble).

class MDAnalysis.analysis.lineardensity.LinearDensity(select, grouping='atoms', binsize=0.25, **kwargs)[source]

Linear density profile

Parameters

  • select (AtomGroup) – any atomgroup

  • grouping (str {'atoms', 'residues', 'segments', 'fragments'}) – Density profiles will be computed on the center of geometry of a selected group of atoms

  • binsize (float) – Bin width in Angstrom used to build linear density histograms. Defines the resolution of the resulting density profile (smaller –> higher resolution)

  • verbose (bool (optional)) – Show detailed progress of the calculation if set to True; the default is False.

results

Keys ‘x’, ‘y’, and ‘z’ for the three directions. Under these keys, find ‘pos’, ‘pos_std’ (mass-weighted density and standard deviation), ‘char’, ‘char_std’ (charge density and its standard deviation), ‘slice_volume’ (volume of bin).

Type

dict

Example

First create a LinearDensity object by supplying a selection, then use the run() method:

ldens = LinearDensity(selection)
ldens.run()

New in version 0.14.0.

Changed in version 1.0.0: Support for the start, stop, and step keywords has been removed. These should instead be passed to LinearDensity.run(). The save() method was also removed, you can use np.savetxt() or np.save() on the LinearDensity.results dictionary contents instead.

Changed in version 1.0.0: Changed selection keyword to select

Parameters

  • trajectory (mda.Reader) – A trajectory Reader

  • verbose (bool, optional) – Turn on more logging and debugging, default False

Changed in version 1.0.0: Support for setting start, stop, and step has been removed. These should now be directly passed to AnalysisBase.run().