Molecular dynamics simulation trajectory of an anionic lipid bilayer: 100 mol% POPS with Na+ counterions using ff99 ions

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: Amber ff99 [J Åqvist J. Phys. Chem. 94 8021 (1990)].

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).