A method to construct the dynamic landscape of a bio-membrane with experiment and simulation

MD simulations of palmitoyl-oleoyl-phosphatidylcholine (POPC) bilayers are provided (3 simulations).

Simulation 1: 256 POPC molecules, 10.2 μs

Simulation 2: 1024 POPC molecules, 9.5 μs

Simulation 1: 4096 POPC molecules, 2.0 μs

All simulations:

42.1875 waters per POPC molecule (50 wt%) and 0.1 M NaCl

Software/Force Field/Water Model: GROMACS 2019.2 or newer with CHARMM36 and TIP3 water

Temperature/Pressure: NPT ensemble at 298.15 K and 1.0 Bar

Time step: 2 fs (recorded timestep provided here is 10 ns)

Energy minimization with the steepest descents algorithm and 1000 kJ mol^-1 nm^-1 as the threshold.

Electrostatic interactions treated with particle-mesh Ewald, with cutoff distance of 10 Å. Bonds with hydrogen constrained with LINCS.