BilayerAnalyzer analysis: `lipid_tilt` - Lipid tilt using the lipid vectors.¶

Description¶

Estimate the lipids tilt angles using the defined lipid vector.

This analyis estimates the mean lipid tilt using the vector represetation of the specified lipids in reference to a particular axis, typically the bilayer normal.

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

Initiated by instance of:¶

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

Syntax¶

lipid_tilt analysis-ID keyword value

lipid_tilt = 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’
- resname (str): Specify the resname of the lipid type to include in this analysis. Default: ‘all’, averages over all lipid types.
- style (str: ‘angle’, ‘order’): Specify whether to compute the tilt angle (‘angle’) or the tilt angle order parameter (‘order’). Default: ‘angle’
- ref_axis (str: ‘x’, ‘y’, or ‘z’): Specify the reference axis that should be used to estimate the tilt. This is typically the axis along the bilayer normal. Default: ‘z’

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_tilt lipid_tilt_1') 

Add by string - adjust a setting:

analyzer.add_analysis('lipid_tilt lipid_tilt_1 leaflet upper')

Add by list:

analyzer.add_analysis(list(['lipid_tilt', 'lipid_tilt_1', dict({'leaflet':'upper'})]))

Add by dict:

analyzer.add_analysis(dict({'analysis_key': 'lipid_tilt', 'analysis_id': 'lipid_tilt_1','analysis_settings':dict({'leaflet':'upper'})}))

To remove from analyzer:

analyzer.remove_analysis('lipid_tilt_1')

Output Info:¶

Retrieve output after running analyses:

output = analyzer.get_analysis_data('lipid_tilt_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_tilt - Lipid tilt using the lipid vectors.¶