All-atom molecular dynamics of the cyanopodophage A4 portal-tail complex reveals dynamic asymmetry in tail fiber chains

This dataset contains all input and output files for a 250 ns all-atom molecular dynamics simulation of the cyanopodophage A4 portal-tail complex. System: Starting structure: PDB 9K09 48 protein chains organized into four protein families: portal (12 chains), adaptor (12 chains), nozzle (6 chains), and tail fibers (18 chains) Approximately 4 million atoms total (protein + TIP3P water + 0.15 M NaCl) Software and force field: GROMACS 2025.2 AMBER force field TIP3P water model Simulation protocol: Energy minimization Multi-stage equilibration: 2 NVT stages followed by 4 NPT stages Production: 250 ns at 310 K and 1 atm, NPT ensemble, 2 fs timestep Contents (125 files, ~40 GB uncompressed): System setup: solvated.gro, ions.mdp, ions.gro Energy minimization: em.mdp, em.gro Equilibration: nvt[1-2].{mdp,edr,gro}, npt[1-4].{mdp,edr,gro} Production: prod.mdp, prod.tpr, prod.xtc (38.7 GB trajectory), prod.edr, prod.cpt Topology: topol.top with 96 chain-specific .itp files (48 position restraint files and 48 per-chain topology files)