BilayerAnalyzer analysis: `flip_flop` - Count lipid flip flops.¶

Description¶

Count any lipid flips flops between the leaflets.

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

Initiated by instance of:¶

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

Syntax¶

flip_flop analysis-ID

flip_flop = 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('flip_flop flip_flop_1') 

Add by string - adjust a setting:

analyzer.add_analysis('flip_flop flip_flop_1 none None')

Add by list:

analyzer.add_analysis(list(['flip_flop', 'flip_flop_1', dict({'none':None})]))

Add by dict:

analyzer.add_analysis(dict({'analysis_key': 'flip_flop', 'analysis_id': 'flip_flop_1','analysis_settings':dict({'none':None})}))

To remove from analyzer:

analyzer.remove_analysis('flip_flop_1')

Output Info:¶

Retrieve output after running analyses:

output = analyzer.get_analysis_data('flip_flop_1')

The output is type <type 'dict'>

References¶

Andrey A. Gurtovenko, and Ilpo Vattulainen, Molecular Mechanism for Lipid Flip-Flops, The Journal of Physical Chemistry B, 2007 111 (48), 13554-13559, DOI: 10.1021/jp077094k http://pubs.acs.org/doi/abs/10.1021/jp077094k?journalCode=jpcbfk
Nicolas Sapay, W. F. Drew Bennett, and D. Peter Tieleman, Molecular Simulations of Lipid Flip-Flop in the Presence of Model Transmembrane Helices, Biochemistry, 2010 49 (35), 7665-7673, DOI: 10.1021/bi100878q http://pubs.acs.org/doi/abs/10.1021/bi100878q

BilayerAnalyzer analysis: flip_flop - Count lipid flip flops.¶