BilayerAnalyzer analysis: `disp_vec` - Displacement vectors.¶

Description¶

Comute displacement vectors for each lipid in the specified leaflet(s) of bilayer.

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

Initiated by instance of:¶

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

Syntax¶

disp_vec analysis-ID keyword value

disp_vec = analysis-Key - keyword/name for this analysis.
analysis-ID = The unique name/ID being assigned to this analysis.
keyword value = settings keyword value pairs
- scale (bool): Specify whether to scale the coordinates by the box dimensions of the reference frame. Default: False
- interval (int): Sets the frame interval over which to compute the displacement vectors.
- leaflet (str: ‘both’, ‘upper’, or ‘lower’): Specifies the bilayer leaflet to include in the estimate. Default: ‘both’
- wrapped (bool): Specify whether to use the wrapped (‘True’) or un-wrapped (‘False’) coordintes for the base of the vectors. Default: False
- resname (str): Specify the resname of the lipid type to include in this analysis. Default: ‘all’, includes all lipid types.
- scale_to_max (bool): Specify whether to scale the coordinates by the box dimensions of the maximum box size in the anlysis. Default: False.

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('disp_vec disp_vec_1') 

Add by string - adjust a setting:

analyzer.add_analysis('disp_vec disp_vec_1 scale False')

Add by list:

analyzer.add_analysis(list(['disp_vec', 'disp_vec_1', dict({'scale':False})]))

Add by dict:

analyzer.add_analysis(dict({'analysis_key': 'disp_vec', 'analysis_id': 'disp_vec_1','analysis_settings':dict({'scale':False})}))

To remove from analyzer:

analyzer.remove_analysis('disp_vec_1')

Output Info:¶

Retrieve output after running analyses:

output = analyzer.get_analysis_data('disp_vec_1')

The output is type <type 'list'>

Note

The real frame ```interval``` setting needs to be a multiple of the frame looping interval set within the BilayerAnalyzer instance (i.e., analyzer.frame_range[2]) for this analysis to work properly.

References¶

Emma Falck, Tomasz Rog, Mikko Karttunen, and Ilpo Vattulainen, Lateral Diffusion in Lipid Membranes through Collective Flows, Journal of the American Chemical Society, 2008 130 (1), 44-45 DOI: 10.1021/ja7103558

BilayerAnalyzer analysis: disp_vec - Displacement vectors.¶