Amber Lipid17 Simulations of POPC/POPS Membranes with NaCl
Description
System: Simulations of POPC/POPS (5:1, 144 lipids in total) membranes with 500, 1000, 2000, 3000, and 4000 mM of NaCl.
Number of POPS: 24.
Number of POPC 120.
Number of waters: 5760.
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 models: 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: 1.
Trajectory lengths per repeat: 200 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).
Notes
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