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'
<class 'pybilt.bilayer_analyzer.analysis_protocols.APLBoxProtocol'>
apl_box analysis-ID
- apl_box = analysis-Key - keyword/name for this analysis.
- analysis-ID = The unique name/ID being assigned to this analysis.
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')
Retrieve output after running analyses:
output = analyzer.get_analysis_data('apl_box_1')
The output is type <type 'numpy.ndarray'>
- 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)