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.
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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:
- license:
- reference:
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 aIOErrorif 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.