Molecular dynamics simulation trajectory of a cationic lipid bilayer: 50/50 mol% DMTAP/DMPC in 1.0 M NaCl

System: Symmetric bilayer of cationic DMTAP (dimyristoyltrimethylammoniumpropane, 50 mol-%) and zwitterionic DMPC (dimyristoylphosphatidylcholine, 50 mol-%) lipids in 1.0 M NaCl solution.

Number of DMPC: 64.
Number of DMTAP: 64.
Number of Na+-ions: 94.
Number of Cl--ions: 158.
Number of waters: 5148.

Lipid model: 'Berger' united-atom [Biophys. J. 72 2002 (1997)] with DMTAP modification by Gurtovenko et al. [Biophys. J. 86 3461 (2004)].
Water model: SPC [In Intermolecular Forces, ed. Pullman. 331 (1981)].

Simulation engine: Gromacs 3.x [www.gromacs.org]

Trajectory length: 170 ns.
Previously equilibrated for: 21 ns.
Sampling rate: every 10 ps.

Time integration step: 2 fs.

Thermodynamic ensemble: NpT.
Temperature coupling: 'Berendsen' [J. Chem. Phys. 81 3684 (1984)] with lipids and water coupled separately at T = 323 K.
Pressure coupling: 'Berendsen' [J. Chem. Phys. 81 3684 (1984)] with xy and z coupled separately at p = 1.0 bar.

Electrostatics: PME [J. Chem. Phys. 98 10089 (1993); J. Chem. Phys. 103 8577 (1995)], real-space cutoff at 1.0 nm.
Van der Waals: Truncated at 1.0 nm.

Constraints: Covalent bond lengths in lipids using LINCS [J. Comput. Chem. 18 1463 (1997)], in water using SETTLE [J. Comput. Chem. 13 952 (1992)].

Used in publications: [1] Markus S. Miettinen, Andrey A. Gurtovenko, Ilpo Vattulainen, and Mikko Karttunen: "Ion Dynamics in Cationic Lipid Bilayer Systems in Saline Solutions". J. Phys. Chem. B 113 9226 (2009). DOI: 10.1021/jp810233q. [2] Markus S. Miettinen: "Computational Modeling of Cationic Lipid Bilayers in Saline Solutions". PhD Thesis. Aalto University School of Science and Technology, Helsinki, Finland. (2010). ISBN 978-952-60-3194-1.