BilayerAnalyzer analysis: `ald` - Average lateral displacement.¶

Description¶

Estimate the average lateral displacement of lipids.

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

Initiated by instance of:¶

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

Syntax¶

ald analysis-ID keyword value

ald = 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: ‘both’, ‘upper’, or ‘lower’): Specifies the bilayer leaflet to include in the estimate. Default: ‘both’
- resname (str): Specify the resname of the lipid type to include in this analysis. Default: ‘all’, includes all lipid types.

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('ald ald_1') 

Add by string - adjust a setting:

analyzer.add_analysis('ald ald_1 leaflet both')

Add by list:

analyzer.add_analysis(list(['ald', 'ald_1', dict({'leaflet':'both'})]))

Add by dict:

analyzer.add_analysis(dict({'analysis_key': 'ald', 'analysis_id': 'ald_1','analysis_settings':dict({'leaflet':'both'})}))

To remove from analyzer:

analyzer.remove_analysis('ald_1')

Output Info:¶

Retrieve output after running analyses:

output = analyzer.get_analysis_data('ald_1')

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

References¶

Kenichiro Koshiyama, Tetsuya Kodama, Takeru Yano, Shigeo Fujikawa, “Molecular dynamics simulation of structural changes of lipid bilayers induced by shock waves: Effects of incident angles”, Biochimica et Biophysica Acta (BBA) - Biomembranes, Volume 1778, Issue 6, June 2008, Pages 1423-1428

BilayerAnalyzer analysis: ald - Average lateral displacement.¶