BilayerAnalyzer analysis: `mass_dens` - Mass density profile.¶

Description¶

Estimate the mass density profile for the specified selection.

This protocol is used to estimate the 1-dimensional mass density profile for a selection of atoms along the bilayer normal. The profile is automatically centered on the bilayer’s center of mass along the bilayer normal.

This protocol is identified by the analysis key: ‘mass_dens’

Initiated by instance of:¶

<class 'pybilt.bilayer_analyzer.analysis_protocols.MassDensProtocol'>

Syntax¶

mass_dens analysis-ID keyword value

mass_dens = analysis-Key - keyword/name for this analysis.
analysis-ID = The unique name/ID being assigned to this analysis.
keyword value = settings keyword value pairs
- n_bins (int): Set the number of bins to divide the normal dimensions into for binning. Defalt: 25
- selection_string (str): Provide the MDAnalysis compatible selection for the atoms to include in this analysis. Default: ‘BILAYER’, use all the lipids of the bilayer as recovered from the selection given to the external BilayerAnalyzer.

Examples¶

Construct analyzer:

analyzer = BilayerAnalyzer(structure='name_of_structure_file',
                           trajectory='name_of_traj_file',
                           selection='resname POPC DOPC')

Add by string - use default settings:

analyzer.add_analysis('mass_dens mass_dens_1') 

Add by string - adjust a setting:

analyzer.add_analysis('mass_dens mass_dens_1 n_bins 25')

Add by list:

analyzer.add_analysis(list(['mass_dens', 'mass_dens_1', dict({'n_bins':25})]))

Add by dict:

analyzer.add_analysis(dict({'analysis_key': 'mass_dens', 'analysis_id': 'mass_dens_1','analysis_settings':dict({'n_bins':25})}))

To remove from analyzer:

analyzer.remove_analysis('mass_dens_1')

Output Info:¶

Retrieve output after running analyses:

output = analyzer.get_analysis_data('mass_dens_1')

The output is type <type 'tuple'>

References¶

None

BilayerAnalyzer analysis: mass_dens - Mass density profile.¶