Gromacs Md · huc-he bundle Automate GROMACS molecular dynamics (MD) simulations end-to-end. Use when the user wants to set up, run, debug, or analyze MD simulations with GROMACS/gmx, including protein, protein-ligand, peptide, nucleic-acid, or membrane systems; build topologies and .mdp files; run pdb2gmx, solvate, genion, grompp, mdrun; perform energy minimization, NVT/NPT equilibration, and production runs with GPU acceleration; analyze trajectories (RMSD, RMSF, Rg, hydrogen bonds, contacts, free energy); or troubleshoot GROMACS errors. Also triggered by Chinese requests containing GROMACS, gmx, or 分子动力学模拟, and Japanese requests containing 分子動力学シミュレーション.
