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Molecular dynamics simulation trajectory of a fully hydrated DMPC lipid bilayer

System: DMPC (dimyristoylphosphatidylcholine) bilayer in water. Number of lipids: 128. Number of waters: 5097. Lipid model: 'Berger' united-atom [Biophys. J. 72 2002 (1997)]. Water model: SPC [In Intermolecular Forces, ed. Pullman. 331 (1981)]. Simulation engine: Gromacs 3.x [www.gromacs.org] Trajectory length: 110 ns. Previously equilibrated for: 20 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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Reuse readiness: 8
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Topics

DMPC lipid bilayer Molecular Dynamics Simulation Gromacs