BilayerAnalyzer analysis: `spatial_velocity_corr` - Weighted average of displacement vector correlations.¶

Description¶

Compute spatial correlation function between lipid displacements/pseudo-velocities.

This analysis computes the displacement vectors as in the ‘disp_vec’ analysis, and uses those to estimated a spatial correlation function between the displacments/pseudo-velocities; the function is of the radial separation between the base of each vector in the bilayers lateral plane. The correlation is the cos(theta) value for the angle theta between the vectors.

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

Initiated by instance of:¶

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

Syntax¶

spatial_velocity_corr analysis-ID keyword value

spatial_velocity_corr = 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
- interval (int): Sets the frame interval over which to compute the displacement vectors.
- 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. Special names are ‘first’ and ‘all’, which use the first and all lipid types respectively. 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. Special names are ‘first’ and ‘all’, which use the first and all lipid types respectively. 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('spatial_velocity_corr spatial_velocity_corr_1') 

Add by string - adjust a setting:

analyzer.add_analysis('spatial_velocity_corr spatial_velocity_corr_1 n_bins 25')

Add by list:

analyzer.add_analysis(list(['spatial_velocity_corr', 'spatial_velocity_corr_1', dict({'n_bins':25})]))

Add by dict:

analyzer.add_analysis(dict({'analysis_key': 'spatial_velocity_corr', 'analysis_id': 'spatial_velocity_corr_1','analysis_settings':dict({'n_bins':25})}))

To remove from analyzer:

analyzer.remove_analysis('spatial_velocity_corr_1')

Output Info:¶

Retrieve output after running analyses:

output = analyzer.get_analysis_data('spatial_velocity_corr_1')

The output is type <type 'tuple'>

Note

The radial distance is centered on lipids of type resname_1 and averaging is taken over the pair-wise interactions of lipids of type ```resname_1``` with lipids of type ```resname_2```.

References¶

None

BilayerAnalyzer analysis: spatial_velocity_corr - Weighted average of displacement vector correlations.¶