All-atom MD trajectory TOCL:POPC (10%), 50mM KCl

<p>500-ns MD simulation of a lipid bilayer, which monolayer was composed of 47 POPC (1-Palmitoyl-2-oleoylphosphatidylcholine)&nbsp;molecules and 3 TLCL (tetra-linoeoyl-cardiolipin)&nbsp;molecules. The background electrolyte is KCl; these ions were added in that amount, which&nbsp;imitates 50-mM ionic force&nbsp;in the bulk. The water amount is large (more than 100 water molecules per lipid), allowing it to equilibrate the electric double layer at a relatively low ionic force.</p> <p>TIP3P water model and CHARMM36 force field were used;&nbsp;the double-deprotonated form of cardiolipin was used (TLCL2). Production&nbsp;simulation was performed with MD integrator (2-fs step, bonds to hydrogen atoms were constrained), Nose-Hoover thermostat (303K, 1-ps time constant)&nbsp;and Parinello-Rahman semi-isotropic barostat (5-ps time constant, water compressibility). PME was used for electrostatics; cut-off radii were set to 1.2 nm. VDW switch radius was set to 1.0 nm.</p> <p>Resulting trajectories&nbsp;deposited:</p> <ul> <li><strong>COMBINED-25ps.trr</strong> [500 ns length, 50-ps step, with velocities] (50, not 25!,&nbsp;<em>filename is improper!</em>)</li> <li><strong>COMBINED-10ps-100ns.trr</strong>&nbsp;[last 100 ns, 10-ps step, with velocities]</li> <li><strong>COMBINED.edr</strong> [500 ns length,&nbsp;2-ps step]</li> </ul> <p>The additional ZIP archive contains intermediate TPR and MDP files and a force field folder.</p>