BilayerAnalyzer analysis: `com_lateral_rdf` - Lipid-lipid RDF in the bilayer lateral plane.¶

Description¶

Estimate the 2-d radial pair distribution function in the bilayer lateral plane using the lipid centers of mass.

This analysis protocol uses the ‘com_frame’ representation.

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

Initiated by instance of:¶

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

Syntax¶

com_lateral_rdf analysis-ID keyword value

com_lateral_rdf = analysis-Key - keyword/name for this analysis.
analysis-ID = The unique name/ID being assigned to this analysis.
keyword value = settings keyword value pairs
- n_bins (int): Specifies the number of bins to use when estimating the RDF. Default: 25
- range_outer (float): Specify the outer distance cutoff for the RDF. Default: 25.0
- leaflet (str: ‘both’, ‘upper’, or ‘lower’): Specifies the bilayer leaflet to include in the estimate. Default: ‘both’
- range_inner (float): Specify the inner distance cutoff for the RDF. Default: 0.0
- 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('com_lateral_rdf com_lateral_rdf_1') 

Add by string - adjust a setting:

analyzer.add_analysis('com_lateral_rdf com_lateral_rdf_1 n_bins 25')

Add by list:

analyzer.add_analysis(list(['com_lateral_rdf', 'com_lateral_rdf_1', dict({'n_bins':25})]))

Add by dict:

analyzer.add_analysis(dict({'analysis_key': 'com_lateral_rdf', 'analysis_id': 'com_lateral_rdf_1','analysis_settings':dict({'n_bins':25})}))

To remove from analyzer:

analyzer.remove_analysis('com_lateral_rdf_1')

Output Info:¶

Retrieve output after running analyses:

output = analyzer.get_analysis_data('com_lateral_rdf_1')

The output is type <type 'tuple'>

References¶

Microsecond Molecular Dynamics Simulations of Lipid Mixing Chunkit Hong, D. Peter Tieleman, and Yi Wang Langmuir 2014 30 (40), 11993-12001 DOI: 10.1021/la502363b http://pubs.acs.org/doi/abs/10.1021/la502363b

BilayerAnalyzer analysis: com_lateral_rdf - Lipid-lipid RDF in the bilayer lateral plane.¶