<jupyter_start><jupyter_text>Stage 1: Energy MinimizationIn this stage, the initial configuration is relaxed using the steepest descent method in order to remove bad contacts. The see the input script (`em.mdp`) for details.<jupyter_code>!gmx grompp -f em.mdp -c ../start.gro -p ../system.top -n ../index.ndx -o run.tpr -maxwarn 2
!gmx mdrun -s run.tpr<jupyter_output><empty_output>
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{'chain_length': '1', 'dir': 'jupyter-structured-clean-dedup', 'id': '275337', 'license': 'MIT', 'n_tokens_mistral': 138, 'n_tokens_neox': 130, 'n_words': 47, 'path': 'workflow/simulation/1_em/em.ipynb', 'repo_name': 'uppittu11/true_lipids', 'size': '382'}