T4 lysozyme, 1-micro second x 8 trajectories

T4 lysozyme<br>T4 lysozyme (164 residues) in water solutionAMBER14 force field and TIP3P water model.As the initial structures: an open state structure (PDB ID 150L) and a closed state structure (2LZM) were adopted.The number of ions was decided by the SLTCAP server. The concentration is0.150~M.Preparation and equilibration scripts were can be available as follws.https://github.com/fazzz/preparation<br>12844 molecules (39827 atoms)Virtual sites were used in some of the molecules.Hydrogen mass repartioning method was use.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 64 x 64 x 64 cells was used with 4th order B-spline interpolation.A single cut-off of 1.273 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: t4lw_open.top, t4lw_close.topMD input of production run: production.mdpjob script:production_job.shproduction tpr: production_open.tpr, production_close.tprtrajectories of production run: superimposed_1micros-10ns_open_[A,B].xtc, superimposed_1micros-10ns_close_[A-C].xtcanimation: production_open_[A,B].mp4, production_close_[A-C].mp4YMMY-AIST-MacBook-Pro:~/Papers/.../MD/production%