Molecular Dynamics Trajectories of Fs, (AAQAA)3 and HP35

The dataset contains 72 explicit-solvent molecular dynamics production trajectories of Fs, (AAQAA)3 and HP35. Each system has four starting conformations, three random-seed replicates and two force-field and water-model protocols, AMBER99SB-ILDN and CHARMM36 using the OpenMM 2024 CHARMM parameter distribution. Each trajectory spans 500 ns, giving 36 microseconds in total. Each ZIP contains a complete 500 ns protein-atom trajectory sampled every 10 ps, stored as NPZ chunks together with the PDB topology, atom mapping and simulation metadata. Coordinates are in nanometers as float32 arrays, with float64 time and periodic box vectors. Associated code repository: https://github.com/wyqmath/protein-backbone-elasticity. File naming: SYSTEM_FORCEFIELD_startNN_repeatNN.zip. SYSTEM is Fs, AAQAA3 for (AAQAA)3, or HP35. FORCEFIELD is AMBER99SB-ILDN or CHARMM36. For each system, start01 to start04 identify its four initial conformations, consistently across both force fields. The original descriptive identifier is retained as start_id in trajectory.json inside each archive. repeat01 to repeat03 identify the three independent random-seed replicates. Every archive contains a 500 ns trajectory.