BilayerAnalyzer analysis: ac - Isothermal area compressibility.

Description

Estimate the isothermal area compressibility.

This protocol is used to estimate the area compressibility modulus, K_A^-1 = [(kT) / var(A)]^-1 , where A is the area in the lateal dimension of the bilayer.

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

Initiated by instance of:

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

Syntax

ac analysis-ID keyword value

  • ac = analysis-Key - keyword/name for this analysis.

  • analysis-ID = The unique name/ID being assigned to this analysis.

  • keyword value = settings keyword value pairs

    • temperature (float): The absolute temperature that the simulation was run at (i.e. in Kelvin). Default: 298.15 K

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('ac ac_1')

Add by string - adjust a setting:

analyzer.add_analysis('ac ac_1 temperature 298.15')

Add by list:

analyzer.add_analysis(list(['ac', 'ac_1', dict({'temperature':298.15})]))

Add by dict:

analyzer.add_analysis(dict({'analysis_key': 'ac', 'analysis_id': 'ac_1','analysis_settings':dict({'temperature':298.15})}))

To remove from analyzer:

analyzer.remove_analysis('ac_1')

Output Info:

Retrieve output after running analyses:

output = analyzer.get_analysis_data('ac_1')

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

Note

Area compressibility is the inverse of area compressibility modulus (see Ref.1).

References

  1. Yoshimichi Andoha, Susumu Okazakia, Ryuichi Ueokab, “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. https://doi.org/10.1016/j.bbamem.2013.01.005