Amber Lipid17 Simulations of POPC/POPS Membranes with NaCl Counterions

<p><strong>System:&nbsp;</strong>Simulations of POPC/POPS (5:1, 144 lipids in total) membranes with NaCl counterions.</p> <p><strong>Number of POPS:</strong>&nbsp;24.</p> <p><strong>Number of POPC</strong>&nbsp;120.</p> <p><strong>Number of waters:</strong>&nbsp;5760.</p> <p><strong>Number of NaCl&nbsp;ions:&nbsp;</strong>24</p> <p><strong>Lipid model:</strong>&nbsp;Amber Lipid 17 [IR&nbsp;Gould, AA Skjevik, CJ Dickson, BD Madej, RC&nbsp;Walker:&nbsp;&quot;Lipid17: A Comprehensive AMBER Force Field for the Simulation of Zwitterionic and Anionic Lipids&quot;&nbsp;in prep.&nbsp;(2018)].</p> <p><strong>Ion models:&nbsp;</strong>&nbsp;Amber ff99 [J&nbsp;&Aring;qvist&nbsp;<em>J. Phys. Chem.</em>&nbsp;<strong>94</strong>&nbsp;8021 (1990)].</p> <p><strong>Water model:</strong>&nbsp;TIP3P&nbsp;[WL&nbsp;Jorgensen,&nbsp;J Chandrasekhar, JD&nbsp;Madura, RW&nbsp;Impey, ML&nbsp;Klein&nbsp;<em>J. Chem. Phys.</em>&nbsp;<strong>79</strong>&nbsp;926 (1983)].</p> <p><strong>Simulation engine:</strong>&nbsp;Amber16 [DA&nbsp;Case et al.&nbsp;<em>AMBER 2017</em>&nbsp;UCSF&nbsp;(2017)].</p> <p><strong>Number of independent repeats per setup:&nbsp;</strong>2.<br> <strong>Trajectory lengths per repeat:</strong>&nbsp;200 ns.<br> <strong>Previously equilibrated for:</strong>&nbsp;300&nbsp;ns.<br> <strong>Sampling rate:</strong>&nbsp;every 10 ps.</p> <p><strong>Time integration step:</strong>&nbsp;2 fs.</p> <p><strong>Thermodynamic ensemble:</strong>&nbsp;NpT.&nbsp;<br> <strong>Temperature coupling:</strong>&nbsp;&#39;Langevin&#39;&nbsp;at T = 298&nbsp;K.<br> <strong>Pressure coupling: &#39;</strong>Berendsen&#39; [<em>J. Chem. Phys.</em>&nbsp;<strong>81</strong>&nbsp;3684 (1984);&nbsp;<em>J. Chem. Phys.</em>&nbsp;<strong>103</strong>&nbsp;10252 (1995)] with xy and z coupled separately at p = 1.0 bar with no&nbsp;surface tension.</p> <p><strong>Electrostatics:&nbsp;</strong>PME [<em>J. Chem. Phys.</em>&nbsp;<strong>98</strong>&nbsp;10089 (1993);<em>&nbsp;J. Chem. Theory Comput.</em>&nbsp;<strong>9</strong>&nbsp;3878 (2013)].<br> <strong>Van der Waals:</strong>&nbsp;Turned off between&nbsp;1.0 nm and 1.5 nm.</p> <p><strong>Constraints:&nbsp;</strong>Lengths&nbsp;of covalent&nbsp;bonds involving Hydrogens&nbsp;in lipids using SHAKE&nbsp;[<em>J. Comput. Phys.</em>&nbsp;<strong>23</strong>&nbsp;327 (1977)], in water using SETTLE [<em>J. Comput. Chem.&nbsp;</em><strong>13</strong>&nbsp;952 (1992)].</p> <p><strong>Used in publications:&nbsp;</strong>OHS&nbsp;Ollila et al. &quot;NMRlipids IV: Headgroup &amp; glycerol backbone structures, and cation binding in bilayers with PS lipids&quot; in prep (2018).</p>