MD2, 1micro second simulation x 6 trajectories

The myeliod differentiation protein 2 (MD2)<br>three MD simulations for one microsecond-long of MD2 with Lipid A and ligand-free MD2 in water solution.The initial structure for holo state of MD2, the crystal structure (PDB ID 2E59) was adopted.The initial structure for apo state, the ligand molecule was removed from the same structure.The preparation of system was done using CHARMM-GUI web server, and CHARMM36 force field and TIP3P were adopted.Equilibration scripts were can be available as follws.https://github.com/fazzz/preparation_MD2<br>A system of 10291 molecules (33289 atoms) was simulated.<br>A total of 1000 ns were simulated with a time step of 4 fs.Neighbor searching was performed every 20 steps.The PME algorithm was used for electrostatic interactions.with a cut-off of 1.2 nm.A reciprocal grid of 60 x 60 x 60 cells was used with 4th order B-spline interpolation.A single cut-off of 1.274 nm was used for Van der Waals interactions.Pressure coupling was done with the Parrinello-Rahman algorithm.<br>initial gro of production run: final_density_stabilization_open.gro, final_density_stabilization_close.grotopologies of production run: MD2_holo.top, MD2_apo.topMD input of production run: production.mdpjob script:production_job.shproduction tpr: production_holo.tpr, production_apo.tprtrajectories of production run: superimposed_1micros-10ns_holo_[A-C].xtc, superimposed_1micros-10ns_apo_[A-C].xtcanimation: production_holo_[A-C].mp4, production_apo_[A-C].mp4