aaltamimi2

Create, run, and analyze molecular dynamics simulations using GROMACS. Use this skill when the user asks for: (1) System setup and topology preparation, (2) Ligand parameterization and small molecule setup, (3) .mdp parameter file design, (4) Simulation workflows (EM → NVT → NPT → production), (5) HPC job scripts and performance tuning, (6) Trajectory analysis (energy, density, MSD, SASA, RDF), (7) Free energy calculations (umbrella sampling, FEP, PMF), (8) Troubleshooting simulation failures (LINCS, exploding systems, barostat instability, PLUMED errors), (9) Polymer-solvent MD simulations for COSMO-RS analysis.