Published September 12, 2023 | Version v1
Dataset Open

NAMD Trajectory of a Palmitoyl Sphingomyelin Bilayer

Authors/Creators

  • 1. University of Virginia

Description

All-atom PSM bilayer simulated in NPT ensemble with NAMD and the CHARMM36 force field from Doktorova et al. 2020 J. Phys. Chem. B. article (DOI 10.1021/acs.jpcb.0c03389). The trajectory represents the last 117 ns used for analysis where the area per lipid is equilibrated (the file has 5874 frames output every 20 ps). The bilayer has 200 lipids total (100 lipids per leaflet) and is hydrated with 45 waters/lipid. The simulation was done at 55C (328.15K) 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 (3.7 GB)

Name Size
md5:af975573419f095676aed0792f9c3c7f
3.4 kB Download
md5:655d3c8e3e8f453dc3f5f06997e47728
4.0 MB Download
md5:e2d99499d10b541668d3a23ebed76190
11.4 MB Download
md5:e457a084592d909a7f22dde6dfe65629
3.7 GB Download

Additional details

References

  • Doktorova M, Kúcerka N, Kinnun JJ, Pan J, Marquardt D, Scott HL, Venable RM, Pastor RW, Wassall SR, Katsaras J, Heberle FA. 2020. Molecular structure of sphingomyelin in fluid phase bilayers determined by the joint analysis of small-angle neutron and X-ray scattering data. J. Phys. Chem. B. 124:5186-5200. DOI: 10.1021/acs.jpcb.0c03389