BilayerAnalyzer analysis: vcm - Volume compressibility modulus.

Description

Estimate the isothermal volume compressibility modulus.

This protocol is used to estimate the volume compressibility modulus, K_V = (kT) / var(V), where V is the volume.

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

Initiated by instance of:

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

Syntax

vcm analysis-ID keyword value

  • vcm = 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('vcm vcm_1')

Add by string - adjust a setting:

analyzer.add_analysis('vcm vcm_1 temperature 298.15')

Add by list:

analyzer.add_analysis(list(['vcm', 'vcm_1', dict({'temperature':298.15})]))

Add by dict:

analyzer.add_analysis(dict({'analysis_key': 'vcm', 'analysis_id': 'vcm_1','analysis_settings':dict({'temperature':298.15})}))

To remove from analyzer:

analyzer.remove_analysis('vcm_1')

Output Info:

Retrieve output after running analyses:

output = analyzer.get_analysis_data('vcm_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