BilayerAnalyzer analysis: `msd_dist` - Mean squared displacement as a function of distance.¶

Description¶

Compute the MSD over a set time interval as function of nearest distance.

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

Initiated by instance of:¶

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

Syntax¶

msd_dist analysis-ID keyword value

msd_dist = analysis-Key - keyword/name for this analysis.
analysis-ID = The unique name/ID being assigned to this analysis.
keyword value = settings keyword value pairs
- range_inner (float): Specify the inner distance cutoff for the RDF. Default: 0.0
- 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’
- 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.
- 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('msd_dist msd_dist_1') 

Add by string - adjust a setting:

analyzer.add_analysis('msd_dist msd_dist_1 n_bins 25')

Add by list:

analyzer.add_analysis(list(['msd_dist', 'msd_dist_1', dict({'n_bins':25})]))

Add by dict:

analyzer.add_analysis(dict({'analysis_key': 'msd_dist', 'analysis_id': 'msd_dist_1','analysis_settings':dict({'n_bins':25})}))

To remove from analyzer:

analyzer.remove_analysis('msd_dist_1')

Output Info:¶

Retrieve output after running analyses:

output = analyzer.get_analysis_data('msd_dist_1')

The output is type <type 'tuple'>

Note

The anlysis is centered on lipids of the type specified by the ```resname_1```. 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¶

None

BilayerAnalyzer analysis: msd_dist - Mean squared displacement as a function of distance.¶