BilayerAnalyzer analysis: `msd` - Single time origin mean squared displacement.¶

Description¶

Estimate the mean squared displacement from a single time origin.

This analysis computes the mean squared displacement (MSD) versus time of the centers of mass of the specified lipids for a single time origin (i.e. the first frame in the trajectory analysis): MSD(t) = <(r(t) - r_0)^2>_i where the angle brackets denote averaging over all lipids of type i; the lipid type used for the analysis is controlled by the leaflet setting.

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

Initiated by instance of:¶

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

Syntax¶

msd analysis-ID keyword value

msd = analysis-Key - keyword/name for this analysis.
analysis-ID = The unique name/ID being assigned to this analysis.
keyword value = settings keyword value pairs
- leaflet (str: ‘both’, ‘upper’, or ‘lower’): Specifies the bilayer leaflet to include in the estimate. Default: ‘both’
- resname (str): Specify the resname of the lipid type to include in this analysis. Default: ‘all’, averages over all lipid types.

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 msd_1') 

Add by string - adjust a setting:

analyzer.add_analysis('msd msd_1 leaflet both')

Add by list:

analyzer.add_analysis(list(['msd', 'msd_1', dict({'leaflet':'both'})]))

Add by dict:

analyzer.add_analysis(dict({'analysis_key': 'msd', 'analysis_id': 'msd_1','analysis_settings':dict({'leaflet':'both'})}))

To remove from analyzer:

analyzer.remove_analysis('msd_1')

Output Info:¶

Retrieve output after running analyses:

output = analyzer.get_analysis_data('msd_1')

The output is type <type 'numpy.ndarray'>

References¶

Preston B. Moore, Carlos F. Lopez, Michael L. Klein, Dynamical Properties of a Hydrated Lipid Bilayer from a Multinanosecond Molecular Dynamics Simulation, Biophysical Journal, Volume 81, Issue 5, 2001, Pages 2484-2494, ISSN 0006-3495, http://dx.doi.org/10.1016/S0006-3495(01)75894-8. (http://www.sciencedirect.com/science/article/pii/S0006349501758948)
Yoshimichi Andoh, Susumu Okazaki, Ryuichi Ueoka, Molecular dynamics study of lipid bilayers modeling the plasma membranes of normal murine thymocytes and leukemic GRSL cells, Biochimica et Biophysica Acta (BBA) - Biomembranes, Volume 1828, Issue 4, April 2013, Pages 1259-1270, ISSN 0005-2736, https://doi.org/10.1016/j.bbamem.2013.01.005. (http://www.sciencedirect.com/science/article/pii/S0005273613000096)
Section 8.7, http://manual.gromacs.org/documentation/5.1.4/manual-5.1.4.pdf

BilayerAnalyzer analysis: msd - Single time origin mean squared displacement.¶