YiiP equilibrium dataset

The MDAnalysisData.yiip_equilibrium module contains a 9-ns equilibrium MD trajectory and a 90-ns equilibrium MD trajectory of a membrane-protein system. It can be used to study membrane-protein dynamics.

fetch_yiip_equilibrium_short([data_home, …])

Load the YiiP 9 ns equilibrium trajectory

fetch_yiip_equilibrium_long([data_home, …])

Load the YiiP 90 ns equilibrium trajectory

YiiP equilibrium trajectory dataset

Molecular dynamics (MD) trajectory files of the YiiP 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 2018.1, using the CHARMM36 force field, the TIP3P explicit water model, NaCl at approximately 100 mM concentration, and Zinc ions.

Trajectory frames were saved every 100 ps for a total of 9 ns and 90 ns simulated time. The topology contains the whole system (protein, membrane, water and ions).

The topology is contained in the YiiP_system.pdb file. The 9-ns trajectory is contained in the YiiP_system_9ns_center.xtc file. The 90-ns trajectory is contained in the YiiP_system_90ns_center.xtc file.

Notes

Data set characteristics:

size

3.82 GB

number of trajectories

2

number of frames

900 (short), 9000 (long)

number of particles

111815

creator

Shujie Fan, Oliver Beckstein

URL

10.6084/m9.figshare.8202149.v1

license

CC-BY 4.0

reference

[Fan2019]

Fan2019

Fan, Shujie; Beckstein, Oliver (2019): Molecular dynamics trajectory of membrane protein YiiP. figshare. Dataset. MDAnalysis. figshare. Fileset. doi: 10.6084/m9.figshare.8202149.v1

MDAnalysisData.yiip_equilibrium.fetch_yiip_equilibrium_short(data_home=None, download_if_missing=True)[source]

Load the YiiP 9 ns equilibrium trajectory

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>/yiip_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 YiiP equilibrium trajectory dataset for description.

MDAnalysisData.yiip_equilibrium.fetch_yiip_equilibrium_long(data_home=None, download_if_missing=True)[source]

Load the YiiP 90 ns equilibrium trajectory

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>/yiip_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 YiiP equilibrium trajectory dataset for description.