BilayerAnalyzer analysis: `lipid_collinearity` - Lipid-lipid collinearity.¶

Description¶

Estimate the lipid-lipid collinearity angles.

This analysis computes the mean lipid-lipid collinearity angle (or order parameter) using the vector represetation of the specified lipids.

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

Initiated by instance of:¶

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

Syntax¶

lipid_collinearity analysis-ID keyword value

lipid_collinearity = analysis-Key - keyword/name for this analysis.
analysis-ID = The unique name/ID being assigned to this analysis.
keyword value = settings keyword value pairs
- leaflet (str: ‘upper’, or ‘lower’): Specifies the bilayer leaflet to include in the estimate. Default: ‘upper’
- style (str: ‘angle’, ‘order’): Specify whether to compute the tilt angle (‘angle’) or the tilt angle order parameter (‘order’). Default: ‘angle’
- resname_2 (str): Specify the resname of the target lipid type to include in this analysis. Default: ‘first’, the first lipid in the list pulled from the com_frame representation.
- resname_1 (str): Specify the resname of the reference lipid type to include in this analysis. Default: ‘first’, the first lipid in the list pulled from the com_frame representation.

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('lipid_collinearity lipid_collinearity_1') 

Add by string - adjust a setting:

analyzer.add_analysis('lipid_collinearity lipid_collinearity_1 leaflet upper')

Add by list:

analyzer.add_analysis(list(['lipid_collinearity', 'lipid_collinearity_1', dict({'leaflet':'upper'})]))

Add by dict:

analyzer.add_analysis(dict({'analysis_key': 'lipid_collinearity', 'analysis_id': 'lipid_collinearity_1','analysis_settings':dict({'leaflet':'upper'})}))

To remove from analyzer:

analyzer.remove_analysis('lipid_collinearity_1')

Output Info:¶

Retrieve output after running analyses:

output = analyzer.get_analysis_data('lipid_collinearity_1')

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

References¶

Anton O. Chugunov, Pavel E. Volynsky, Nikolay A. Krylov, Ivan A. Boldyrev, and Roman G. Efremov, Liquid but Durable: Molecular Dynamics Simulations Explain the Unique Properties of Archaeal-Like Membranes, Scientific Reports, 4:7462, 2014, doi:10.1038/srep07462 (https://www.nature.com/articles/srep07462)

BilayerAnalyzer analysis: lipid_collinearity - Lipid-lipid collinearity.¶