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System: Simulations of POPC/POPS (5:1, 144 lipids in total) membranes with various CaCl2 concentrations. Number of POPS: 24. Number of POPC 120. Number of waters: 5760 (excluded from uploaded trajectories) Number of Ca+2 Ions: 52 (500mm), 104 (1000mm), 208 (2000mm), 311 (3000mm), 415 (4000mm) 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: Li/Merz Ions [Li, P. J. Chem. Theory Comput. 9 2733-2748 (2013)]. 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: 200 ns. Previously equilibrated for: 300 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).
B.K acknowledges financial support from International Max Planck Research School on Multiscale Bio-Systems
Phosphatidylcholine, amber lipid 17, anionic lipid bilayer, Phosphatidylserine, molecular dynamics
Phosphatidylcholine, amber lipid 17, anionic lipid bilayer, Phosphatidylserine, molecular dynamics
citations This is an alternative to the "Influence" indicator, which also reflects the overall/total impact of an article in the research community at large, based on the underlying citation network (diachronically). | 2 | |
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influence This indicator reflects the overall/total impact of an article in the research community at large, based on the underlying citation network (diachronically). | Average | |
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