Published September 13, 2023 | Version v1

NAMD Trajectory of a Tetraoleoyl Cardiolipin Bilayer

Authors/Creators

  • 1. University of Virginia

Description

All-atom TOCL (tetraoleoyl cardiolipin) bilayer simulated in NPT ensemble with NAMD and the CHARMM36 force field from Doktorova et al. 2017 Phys. Chem. Chem. Phys. article (DOI 10.1039/c7cp01921a). The trajectory represents the last 155 ns used for analysis where the area per lipid is equilibrated (the file has 7752 frames output every 20 ps). The bilayer has 100 lipids total (50 lipids per leaflet) and is hydrated with 60 waters/lipid and 140mM NaCl. The simulation was done at 30C (303.15K) and the trajectory is centered on the bilayer midplane.

Notes

Attached files include the structure (.psf and .pdb), trajectory (.dcd) and a copy of the NAMD input file with simulation parameters.

Files

Files (4.0 GB)

Name Size
md5:edc70a69762ba2d109cc31da5a9b831c
4.0 kB Download
md5:6f169635b691eb765c21d6a460575621
3.3 MB Download
md5:5ea3401142ad70ce450ed2422a370312
11.9 MB Download
md5:6cdf732a3486a0f3ae3e6958bb0ecf36
4.0 GB Download

Additional details

References

  • Doktorova M, Harries D, and Khelashvili, G. 2017. Determination of bending rigidity and tilt modulus of lipid membranes from real-space fluctuation analysis of molecular dynamics simulations. Phys. Chem. Chem. Phys. 19:16806-16818. DOI: 10.1039/C7CP01921A