BilayerAnalyzer analysis: thickness_leaflet_distance - Distance between the leaflets’ centers of mass along the normal.

Description

Estimate the bilayer thickness using the distance between the COMs of each leaflet.

This analysis uses the COM postions from the com_frame representation. At each frame the centers-of-mass of each leaflet is computed and the distance along the bilayer normal is computed. This is another to estimate the bilayer thickness.

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

Initiated by instance of:

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

Syntax

thickness_leaflet_distance analysis-ID

  • thickness_leaflet_distance = analysis-Key - keyword/name for this analysis.

  • analysis-ID = The unique name/ID being assigned to this analysis.

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('thickness_leaflet_distance thickness_leaflet_distance_1')

Add by string - adjust a setting:

analyzer.add_analysis('thickness_leaflet_distance thickness_leaflet_distance_1 none None')

Add by list:

analyzer.add_analysis(list(['thickness_leaflet_distance', 'thickness_leaflet_distance_1', dict({'none':None})]))

Add by dict:

analyzer.add_analysis(dict({'analysis_key': 'thickness_leaflet_distance', 'analysis_id': 'thickness_leaflet_distance_1','analysis_settings':dict({'none':None})}))

To remove from analyzer:

analyzer.remove_analysis('thickness_leaflet_distance_1')

Output Info:

Retrieve output after running analyses:

output = analyzer.get_analysis_data('thickness_leaflet_distance_1')

The output is type <type 'numpy.ndarray'>

Note

The P-P distance can be estimated for phospholipids by assigning the phosphorous atoms as the reference atoms to the com_frame.

References

None