Molecular dynamics simulation trajectory of a cationic lipid bilayer: 75/25 mol% DMTAP/DMPC

2016-05-20T00:00:00Z (GMT) by Miettinen, Markus S.

System: Symmetric bilayer of cationic DMTAP (dimyristoyltrimethylammoniumpropane, 75 mol-%) and zwitterionic DMPC (dimyristoylphosphatidylcholine, 25 mol-%) lipids in water.

Number of DMPC: 32.
Number of DMTAP: 96.
Number of Cl--ions: 96.
Number of waters: 5496.

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 []

Trajectory length: 109 ns.
Previously equilibrated for: 31 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.




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