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.
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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:
- license:
- 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 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 Peptide in DMPC membrane dataset for description.