Comute displacement vectors for each lipid in the specified leaflet(s) of bilayer.
This protocol is identified by the analysis key: 'disp_vec'
<class 'pybilt.bilayer_analyzer.analysis_protocols.DispVecProtocol'>
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.
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')
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.
- 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