Lipid center-of-mass trajectory: short-time dynamics

This file contains the center-of-mass coordinates of the lipid molecules in a Molecular Dynamics simulation of a hydrated lipid bilayer. The simulated system consists of 2033 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine) molecules and 57952 water beads (equivalent to 231808 water molecules), using the coarse-grained representation of the MARTINI force field. Note that the mass of a POPC molecule is significantly higher (936 g/mol) in this representation than the mass of a real POPC molecule (760 g/mol). The simulation was performed in an NVT ensemble at T = 320 K.

This trajectory stores the short-time dynamics of the lipid centers of masses, sampled at a time step of 0.03 ps up to a total length of 300 ps. The long-time dynamics are available at http://dx.doi.org/10.5281/zenodo.61743.

For a detailed description of the simulation, see the thesis of Sławomir Stachura, available at http://www.theses.fr/2014PA066239

Two analyses of this simulation have already been published:

• S. Stachura and G.R. Kneller Anomalous lateral diffusion in lipid bilayers observed by molecular dynamics simulations with atomistic and coarse-grained force fields Mol. Sim. 40, 245-250 (2014) (http://dx.doi.org/10.1080/08927022.2013.840902)
• S. Stachura and G.R. Kneller Probing anomalous diffusion in frequency space J. Chem. Phys. 143, 191103 (2015) (http://dx.doi.org/10.1063/1.4936129)

This work was funded by the French Agence Nationale de la Recherche (Contract No. ANR- 2010-COSI-01-001).

Trajectory data

The trajectory is stored in an HDF5 file that uses the ActivePapers conventions (http://www.activepapers.org/). Any HDF5-compatible software can be used to read the trajectory data. The ActivePapers software is only required to re-use the included conversion script.

The trajectory is contained in the group
  /data/POPC_martini_nvt

It is stored in H5MD/MOSAIC format. The positions and time labels are contained in the following datasets:
  /data/POPC_martini_nvt/particles/universe/position/value
  /data/POPC_martini_nvt/particles/universe/position/time

For a complete specification of the H5MD/MOSAIC format, see:
  http://nongnu.org/h5md/index.html
  http://mosaic-data-model.github.io/mosaic-specification/h5md_mosaic_module.html

Plots

Two 3D plots are provided to give an overview of the lipid motions:
  /documentation/all_lipids.pdf
  shows all the lipid center-of-mass positions once every 3 ps.
  /documentation/one_lipids.pdf
  shows a single lipid center of mass position every 0.3 ps.