Molecular dynamics simulation trajectory of a cationic lipid bilayer: 75/25 mol% DMTAP/DMPC
收藏资源简介：
<strong>System: </strong>Symmetric bilayer of cationic DMTAP (dimyristoyltrimethylammoniumpropane, 75 mol-%) and zwitterionic DMPC (dimyristoylphosphatidylcholine, 25 mol-%) lipids in water. <strong>Number of DMPC:</strong> 32.<br> <strong>Number of DMTAP:</strong> 96.<br> <strong>Number of Cl--ions:</strong> 96.<br> <strong>Number of waters:</strong> 5496. <strong>Lipid model:</strong> 'Berger' united-atom [<em>Biophys. J.</em> <strong>72</strong> 2002 (1997)] with DMTAP modification by Gurtovenko et al. [<em>Biophys. J. </em><strong>86</strong> 3461 (2004)].<br> <strong>Water model:</strong> SPC [In <em>Intermolecular Forces,</em> ed. Pullman. 331 (1981)]. <strong>Simulation engine:</strong> Gromacs 3.x [www.gromacs.org] <strong>Trajectory length:</strong> 109 ns.<br> <strong>Previously equilibrated for:</strong> 31 ns.<br> <strong>Sampling rate:</strong> every 10 ps. <strong>Time integration step:</strong> 2 fs. <strong>Thermodynamic ensemble:</strong> NpT. <br> <strong>Temperature coupling:</strong> 'Berendsen' [<em>J. Chem. Phys.</em> <strong>81</strong> 3684 (1984)] with lipids and water coupled separately at T = 323 K.<br> <strong>Pressure coupling: '</strong>Berendsen' [<em>J. Chem. Phys.</em> <strong>81</strong> 3684 (1984)] with xy and z coupled separately at p = 1.0 bar. <strong>Electrostatics: </strong>PME [<em>J. Chem. Phys.</em> <strong>98</strong> 10089 (1993); <em>J. Chem. Phys.</em> <strong>103</strong> 8577 (1995)], real-space cutoff at 1.0 nm.<br> <strong>Van der Waals:</strong> Truncated at 1.0 nm. <strong>Constraints: </strong>Covalent bond lengths in lipids using LINCS [<em>J. Comput. Chem.</em> <strong>18</strong> 1463 (1997)], in water using SETTLE [J. Comput. Chem. <strong>13</strong> 952 (1992)]. <strong>Used in publications: </strong>[1] Markus S. Miettinen, Andrey A. Gurtovenko, Ilpo Vattulainen, and Mikko Karttunen: "Ion Dynamics in Cationic Lipid Bilayer Systems in Saline Solutions". <em>J. Phys. Chem. B</em> <strong>113</strong> 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.
