CodeEntropy.ClassCollection.PoseidonClass.Poseidon_mp

class CodeEntropy.ClassCollection.PoseidonClass.Poseidon_mp(container, start=0, end=- 1, step=1, pureAtomNum=1, cutShell=None, excludedResnames=None, water='WAT', verbose=False, thread=4)[source]
__init__(container, start=0, end=- 1, step=1, pureAtomNum=1, cutShell=None, excludedResnames=None, water='WAT', verbose=False, thread=4)[source]

This is a initialization function to collect information from a MDanalysis universe into a data container for analysis using POSEIDON.

Warning

This requires a lot of memory to run with very little performance gain.

Parameters:

  • container (MDAnalyse.Universe) – A Universe object will all topology, dihedrals,coordinates and force information Check Example/create_new_universe.py on how to create a universe from existing data.

  • start (int or None, Optional, default: 0) – Frame id to start analysis.

  • end (int or None, Optional, default: -1) – Frame id to end analysis.

  • step (int, Optional, default: 1) – Steps between frame.

  • pureAtomNum (int, Optional, default: 1) – Reference molecule resid for pure liquid.

  • cutShell (float or None, Optional, default: 1) – Explicit cut off shell. Default to None which uses the relative angular distance (RAD) algorithm. See Jonathan Higham and Richard H. Henchman , “Locally adaptive method to define coordination shell”, J. Chem. Phys. 145, 084108 (2016)

  • excludedResnames (list of str or None, Optional, default: None) – List of resnames to exclude from nearest non alike analysis.

  • water (list of str, Optional, default: “WAT”) – Resname for water molecules.

  • verbose (bool, Optional, default: False) – Print out progress of each step.

  • thread (int, Optional, default: 4) – How many multiprocess thread to spawn

Methods

__init__(container[, start, end, step, ...])

This is a initialization function to collect information from a MDanalysis universe into a data container for analysis using POSEIDON.

run_analysis([temperature, entropyEnergy, ...])

Perform analysis using poseidon