Graph-based analyses of dynamic water-mediated hydrogen-bond networks in phosphatidylserine:cholesterol membranes
Molecular dynamics simulations of POPS lipid bilayers with and without cholesterol.
Steps to reproduce
Simulation details: Software and version: NAMD 2.13 Forcefield and version: CHARMM, c36 Jul 2020 Time step : 1.0 fs Coordinates saved every : 1ns Accumulated simulation time : Last 100ns of 500ns long trajectory Temperature: 310.15K Pressure: 1 bar System setup: Solvent type: TIP3P 0.15M neutralizing KCl salt System 1: pure POPS Number of molecules: Water: 8578 POPS (in each bilayer):109 Total number of atoms: 53680 System 2: POPS_Chol Number of molecules: Water: 8367 POPS (in each bilayer): 98 Cholesterol (in each bilayer): 11 Total number of atoms: 51859
European Union’s Horizon 2020 research and innovation programme