AdK equilibrium dataset

The MDAnalysisData.adk_equilibrium module contains a 1-µs equilibrium MD trajectory of a globular protein with all solvent removed. It can be used to study protein dynamics.

fetch_adk_equilibrium([data_home, …])

Load the AdK 1us equilibrium trajectory (without water)

AdK equilibrium trajectory dataset

MD trajectory of apo adenylate kinase with CHARMM27 force field and simulated with explicit water and ions in NPT at 300 K and 1 bar. Saved every 240 ps for a total of 1.004 µs. Produced on PSC Anton. The trajectory only contains the protein while all solvent was stripped in order to reduce the trajectory size. The whole protein was superimposed on the CORE domain of AdK by RMSD fitting.

The topology is contained in the PSF file (CHARMM format). The trajectory is contained in the DCD file (CHARMM/NAMD format).

Notes

Data set characteristics:

size

161 MB

number of trajectories

1

number of frames

4187

number of particles

3341

creator

Sean Seyler

URL

10.6084/m9.figshare.5108170.v1

license

CC-BY 4.0

reference

[Seyler2017]

Seyler2017

Seyler, Sean; Beckstein, Oliver (2017): Molecular dynamics trajectory for benchmarking MDAnalysis. figshare. Fileset. doi: 10.6084/m9.figshare.5108170.v1

MDAnalysisData.adk_equilibrium.fetch_adk_equilibrium(data_home=None, download_if_missing=True)[source]

Load the AdK 1us 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>/adk_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 AdK equilibrium trajectory dataset for description.