Molecular Dynamics trajectories of membrane protein YiiP

Molecular dynamics (MD) trajectory files of the YiiP membrane protein in a POPE:POPG 4:1 model membrane. The equilibrium simulation was performed in the <i>NPT</i> ensemble at <i>T</i>=300K and<i> P</i>=1 bar. The system was simulated with Gromacs 2018.1, using the CHARMM36 force field, the TIP3P explicit water model, NaCl at approximately 100 mM concentration, and Zinc ions.<br>Trajectory frames were saved every 100 ps for a total of 9 ns and 90ns simulated time. The topology contains the whole system (protein, membrane, water and ions).<br>The topology is contained in the <i>YiiP_system.pdb </i>file. The 9-ns trajectory is contained in the <i>YiiP_system_9ns_center.xtc </i>file. The 90-ns trajectory is contained in the <i>YiiP_system_90ns_center.xtc</i> file.