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

500-ns MD simulation of a lipid bilayer, which monolayer was composed of 47 POPC (1-Palmitoyl-2-oleoylphosphatidylcholine) molecules and 3 TLCL (tetra-linoeoyl-cardiolipin) molecules. The background electrolyte is KCl; these ions were added in that amount, which imitates 50-mM ionic force 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.

TIP3P water model and CHARMM36 force field were used; the double-deprotonated form of cardiolipin was used (TLCL2). Production simulation was performed with MD integrator (2-fs step, bonds to hydrogen atoms were constrained), Nose-Hoover thermostat (303K, 1-ps time constant) 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.

Resulting trajectories deposited:

• COMBINED-25ps.trr [500 ns length, 50-ps step, with velocities] (50, not 25!, filename is improper!)
• COMBINED-10ps-100ns.trr [last 100 ns, 10-ps step, with velocities]
• COMBINED.edr [500 ns length, 2-ps step]

The additional ZIP archive contains intermediate TPR and MDP files and a force field folder.