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Published September 19, 2023 | Version v1
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All-atom Gromacs Trajectory of POPC/TOCL bilayer mixture

Authors/Creators

  • 1. University of Virginia

Description

All-atom bilayer mixture of POPC/TOCL 1:1 simulated in an NPT ensemble with Gromacs and the CHARMM36 force field from Castillo et al, 2022, Mol. Pharmaceutics. 19:1839-1852 (https://doi.org/10.1021/acs.molpharmaceut.1c00926). The trajectory represents 540 ns with frames output every 20 ps. The bilayer has 120 lipids total (60 lipids per leaflet) and is hydrated with 100 waters/lipid and sodium ions to neutralize the system. The simulation was done at 37C (310.15K).

POPC is 16:0,18:1 PC; TOCL is tetraoleoyl cardiolipin

Notes

Attached files include the structure (.gro), trajectory (.xtc) and input gromacs file (.mdp) with simulation parameters for the production run.

Files

Files (5.9 GB)

Name Size
md5:17dd0a03f9580926cc30fe42333e7ada
5.9 GB Download
md5:f11721aa2e00d819753c19036eff73a5
3.2 kB Download
md5:4dd54777374896e19d6e26eb2ba72d8d
4.1 MB Download

Additional details

References

  • Castillo SR, Rickeard BW, DiPasquale M, Nguyen MHL, Lewis-Laurent A, Doktorova M, Kav B, Miettinen MS, Nagao M, Kelley EG, Marquardt D. 2022. Probing the link between Pancratistatin and mitochondrial apoptosis through changes in the membrane dynamics on the nanoscale. Mol. Pharmaceutics. 19:1839-1852. DOI: 10.1021/acs.molpharmaceut.1c00926