title: Molecular dynamics simulation trajectory of an anionic lipid bilayer: 100 mol% POPS with Na+ counterions using Joung-Cheatham Ions
author: Miettinen, Markus S.
description: System: Symmetric bilayer of anionic POPS (palmitoyl-oleoyl-phosphatidylserine 100 mol-%) lipids with sodium (Na+) counter ions. Number of POPS: 128. Number of Na+-ions: 128. Number of waters: 4480. Lipid model: Amber Lipid 17 [IR Gould, AA Skjevik, CJ Dickson, BD Madej, RC Walker: "Lipid17: A Comprehensive AMBER Force Field for the Simulation of Zwitterionic and Anionic Lipids" in prep. (2018)]. Ion model: Joung–Cheatham [IS Joung, TE Cheatham III J. Phys. Chem. B 112 9020 (2008)]. Water model: TIP3P [WL Jorgensen, J Chandrasekhar, JD Madura, RW Impey, ML Klein J. Chem. Phys. 79 926 (1983)]. Simulation engine: Amber16 [DA Case et al. AMBER 2017 UCSF (2017)]. Number of independent repeats per setup: 2. Trajectory lengths per repeat: 400 ns + 100 ns. Previously equilibrated for: 100 ns. Sampling rate: every 10 ps. Time integration step: 2 fs. Thermodynamic ensemble: NpT.  Temperature coupling: 'Langevin' at T = 298 K. Pressure coupling: 'Berendsen' [J. Chem. Phys. 81 3684 (1984); J. Chem. Phys. 103 10252 (1995)] with xy and z coupled separately at p = 1.0 bar with no surface tension. Electrostatics: PME [J. Chem. Phys. 98 10089 (1993); J. Chem. Theory Comput. 9 3878 (2013)]. Van der Waals: Turned off between 1.0 nm and 1.5 nm. Constraints: Lengths of covalent bonds involving Hydrogens in lipids using SHAKE [J. Comput. Phys. 23 327 (1977)], in water using SETTLE [J. Comput. Chem. 13 952 (1992)]. Used in publications: OHS Ollila et al. "NMRlipids IV: Headgroup & glycerol backbone structures, and cation binding in bilayers with PS lipids" in prep (2018).