Luthey-Schulten-Lab/Minimal_Cell_4DWCM — reverse-engineered prompt

Please turn this repo into something I can actually run end to end for the JCVI syn3A 4D whole cell simulation. I want a clean setup flow that checks for the required external tools, makes sure the right conda environment and LAMMPS path are active, and gives me one simple way to launch the main Whole_Cell_Minimal_Cell.py job with the needed inputs like output folder, simulation time, GPU index, DNA software folder, and random seed.

If something is missing, show clear messages instead of failing in a confusing way. Also make the restart workflow easy, using the existing restart script so I can continue a crashed or partial run from a previous output folder. Please keep the science code itself intact, but improve the usability, docs, and example commands so a new person can reproduce a short test run, know what dependencies are required, and understand where outputs and restart files go. If you need to, look up the current install docs for the external tools online.