BilayerAnalyzer analysis: `area_fluctuation` - Bilayer lateral box area fluctuation.¶

Description¶

Estimate the area fluctuation in the box along the bilayer laterals.

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

Initiated by instance of:¶

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

Syntax¶

area_fluctuation analysis-ID

area_fluctuation = 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('area_fluctuation area_fluctuation_1') 

Add by string - adjust a setting:

analyzer.add_analysis('area_fluctuation area_fluctuation_1 none None')

Add by list:

analyzer.add_analysis(list(['area_fluctuation', 'area_fluctuation_1', dict({'none':None})]))

Add by dict:

analyzer.add_analysis(dict({'analysis_key': 'area_fluctuation', 'analysis_id': 'area_fluctuation_1','analysis_settings':dict({'none':None})}))

To remove from analyzer:

analyzer.remove_analysis('area_fluctuation_1')

Output Info:¶

Retrieve output after running analyses:

output = analyzer.get_analysis_data('area_fluctuation_1')

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

References¶

None

BilayerAnalyzer analysis: area_fluctuation - Bilayer lateral box area fluctuation.¶