BilayerAnalyzer analysis: ndcorr - Correlation between bilayer surface curvature and lipid clustering.

Description

Correlation between bilayer surfucace curvature and the clustering of lipid molecules.

This protocol is used to estimate the cross correlation between the normal dimension deflection of lipids and the lipid types in local blocks of the bilayer. This serves as a measure of the correlation between the local curvature and composition of the bilayer.

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

Initiated by instance of:

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

Syntax

ndcorr analysis-ID

  • ndcorr = 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('ndcorr ndcorr_1')

Add by string - adjust a setting:

analyzer.add_analysis('ndcorr ndcorr_1 none None')

Add by list:

analyzer.add_analysis(list(['ndcorr', 'ndcorr_1', dict({'none':None})]))

Add by dict:

analyzer.add_analysis(dict({'analysis_key': 'ndcorr', 'analysis_id': 'ndcorr_1','analysis_settings':dict({'none':None})}))

To remove from analyzer:

analyzer.remove_analysis('ndcorr_1')

Output Info:

Retrieve output after running analyses:

output = analyzer.get_analysis_data('ndcorr_1')

The output is type <type 'dict'>

Note

Automatically estimates the correlations with each lipid type in the bilayer selection provided to the external BilayerAnalyzer object.

References

  1. Koldso H, Shorthouse D, He Lie Sansom MSP (2014) “Lipid Clustering Correlates with Membrane Curvature as Revealed by Molecular Simulations of Complex Lipid Bilayers.” PloS Comput Biol 10(10): e1003911. doi.10.1371/journal.pcbi.1003911