Membrane peptide dataset

The MDAnalysisData.membrane_peptide module contains a 1-ns equilibrium MD trajectory of a short synthetic α-helical peptide in a DMPC membrane with explicit water solvent. It can be used to study protein-lipid interactions and demonstrates the effect of periodic boundary conditions on the atomic coordinates.

fetch_membrane_peptide([data_home, …])

Load the helical peptide in DMPC membrane equilibrium trajectory

Peptide in DMPC membrane dataset

Molecular dynamics simulation of a 19-residue peptide inside a pure DMPC membrane with water at full atomic detail with explicit solvent. The total simulated time is 1 ns.

The simulation was performed in the NPT ensemble at 1 atm at 310K using Berendsen (semi-isotropic) and V-rescale for pressure and temperature coupling, respectively, with 1.6 ps and 0.1 ps as coupling constants. Van der Waals interactions were treated using the Verlet algorithm with a 1 nm cutoff. Electrostatics where treated with particle-mesh Ewald, with a 1 nm cutoff for the real space calculations. Both the peptide and DMPC were parameterized using the GROMOS 54A7 force field, while the SPC model was used for water. LINCS restraints were used on all the bonds.

The peptide sequence is AAAQAAQAQWAQRQATWQA. This sequence was not taken from any real world examples, as this is a test system created for MDAnalysis datasets. The peptide was set to have a α-helical secondary structure, and was inserted manually in the membrane before minimization and equilibration.

The topology is contained in the TPR file (Gromacs format). The trajectory is contained in the XTC file (Gromacs compressed coordinates format).

Notes

Data set characteristics:

size

67 MB

number of trajectories

1

number of frames

1001

number of particles

18727

creator

Davide Cruz

URL

10.6084/m9.figshare.8046437.v1

license

CC-BY 4.0

MDAnalysisData.membrane_peptide.fetch_membrane_peptide(data_home=None, download_if_missing=True)[source]

Load the helical peptide in DMPC membrane 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>/membrane_peptide.

  • 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 Peptide in DMPC membrane dataset for description.