BilayerAnalyzer analysis: acm - Area compressibility modulus.

Description

Estimate the isothermal area compressibility modulus.

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

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

Initiated by instance of:

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

Syntax

acm analysis-ID keyword value

  • acm = 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('acm acm_1')

Add by string - adjust a setting:

analyzer.add_analysis('acm acm_1 temperature 298.15')

Add by list:

analyzer.add_analysis(list(['acm', 'acm_1', dict({'temperature':298.15})]))

Add by dict:

analyzer.add_analysis(dict({'analysis_key': 'acm', 'analysis_id': 'acm_1','analysis_settings':dict({'temperature':298.15})}))

To remove from analyzer:

analyzer.remove_analysis('acm_1')

Output Info:

Retrieve output after running analyses:

output = analyzer.get_analysis_data('acm_1')

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

References

  1. Christofer Hofsab, Erik Lindahl, and Olle Edholm, “Molecular Dynamics Simulations of Phospholipid Bilayers with Cholesterol”, Biophys J. 2003 Apr; 84(4): 2192-2206. doi: 10.1016/S0006-3495(03)75025-5

  2. L. Janosi and A. A. Gorfe, J. Chem. Theory Comput. 2010, 6, 3267-3273

  3. D. Aguayo, F. D. Gonzalez-Nilo, and C. Chipot, J. Chem. Theory Comput. 2012, 8, 1765-1773