NhaA equilibrium dataset

The MDAnalysisData.nhaa_equilibrium module contains a 500-ns equilibrium MD trajectory of a membrane-protein system with all solvent removed. It can be used to study membrane- protein dynamics.

fetch_nhaa_equilibrium([data_home, …])

Load the NhaA 500 ns equilibrium trajectory (without water)

NhaA equilibrium trajectory dataset

Molecular dynamics (MD) trajectory of the NhaA membrane protein in a POPE:POPG 4:1 model membrane. The equilibrium simulation was performed in the NPT ensemble at T=300K and P=1 bar. The system was simulated with Gromacs 5.1.4, using the CHARMM36 force field, the TIP3P explicit water model, and NaCl at approximately 100 mM concentration.

Trajectory frames were saved every 100 ps for a total of 500 ns simulated time. The topology only contains the protein, membrane and ions (because the water molecules were stripped from the trajectory to save space).

The topology is contained in the NhaA_non_water.gro file. The trajectory is contained in the NhaA_non_water.xtc file.

Notes

Data set characteristics:

size

1.07 GB

number of trajectories

1

number of frames

5000

number of particles

60702

creator

Ian Kenney, Shujie Fan

URL

10.6084/m9.figshare.7185203.v2

license

CC-BY 4.0

reference

[Kenney2018]

Kenney2018

M. Kenney, Ian; Fan, Shujie; Beckstein, Oliver (2018): Molecular dynamics trajectory of membrane protein NhaA. figshare. Dataset. MDAnalysis. figshare. Fileset. doi: 10.6084/m9.figshare.7185203.v2

MDAnalysisData.nhaa_equilibrium.fetch_nhaa_equilibrium(data_home=None, download_if_missing=True)[source]

Load the NhaA 500 ns equilibrium trajectory (without water)

Parameters
  • data_home (optional, default: None) – Specify another download and cache folder for the datasets. By default all MDAnalysisData data is stored in ‘~/MDAnalysis_data’ subfolders. This dataset is stored in <data_home>/nhaa_equilibrium.

  • download_if_missing (optional, default=True) – If False, raise a IOError if the data is not locally available instead of trying to download the data from the source site.

Returns

  • dataset (dict-like object with the following attributes:)

  • dataset.topology (filename) – Filename of the topology file

  • dataset.trajectory (filename) – Filename of the trajectory file

  • dataset.DESCR (string) – Description of the trajectory.

See NhaA equilibrium trajectory dataset for description.