Use a new working copy. bash run.sh runs Packmol, GROMACS EM+20ps NVT, LAMMPS EM+20ps NVT and plots on CPU. 216 SPC/E waters. The 20ps trajectories demonstrate topology and initial equilibration, not converged density/transport. Pressure is not controlled in NVT. The two engines use different thermostats and initial velocities; do not treat their trajectories or absolute potential energies as an exact parity test. Input and all needed topology setup are included; existing force fields are referenced from installed GROMACS.
