BilayerAnalyzer analysis: `apl_box` - Area per lipid using box dimensions.¶

Description¶

Estimate the area per lipid using the lateral area.

This analysis is used to estimate the area per lipid (APL) using the lateral box dimensions, A_l = 2<A_xy>/N_l , where A_xy is area of the lateral box dimensions (used to approximate the surface area of the bilayer) and N_l is the number of lipids in the bilayer. As a molar quantity this approach is only accurate for homogenous lipid bilayers. If the bilayer is inhomogenous then this estimate represents a composite average of the area per lipid.

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

Initiated by instance of:¶

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

Syntax¶

apl_box analysis-ID

apl_box = analysis-Key - keyword/name for this analysis.
analysis-ID = The unique name/ID being assigned to this analysis.

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('apl_box apl_box_1') 

Add by string - adjust a setting:

analyzer.add_analysis('apl_box apl_box_1 none None')

Add by list:

analyzer.add_analysis(list(['apl_box', 'apl_box_1', dict({'none':None})]))

Add by dict:

analyzer.add_analysis(dict({'analysis_key': 'apl_box', 'analysis_id': 'apl_box_1','analysis_settings':dict({'none':None})}))

To remove from analyzer:

analyzer.remove_analysis('apl_box_1')

Output Info:¶

Retrieve output after running analyses:

output = analyzer.get_analysis_data('apl_box_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)

BilayerAnalyzer analysis: apl_box - Area per lipid using box dimensions.¶