molecular-dynamics

To run molecular dynamics simulations for protein stability, provide a PDB structure to execute the full OpenMM workflow: system setup, energy minimization, NVT/NPT equilibration, and production MD. This generates time-resolved trajectory data for analyzing biomolecular motions and stability.

Yes, you can compute RMSD, RMSF, contact maps, and free energy surfaces from trajectories using MDAnalysis. The skill integrates trajectory analysis workflows to extract structural insights regarding protein motions and conformational sampling directly from your simulation data.

OpenMM supports protein-ligand binding simulations by building protein or protein-ligand systems and assigning force fields. You can perform energy minimization, NVT and NPT equilibration, and production MD to investigate drug binding interactions and conformational changes.

The best way to analyze free energy surfaces from MD trajectories is by running the integrated trajectory analysis workflow using MDAnalysis. It processes production MD output to calculate energy surfaces, alongside RMSD, RMSF, and contact maps for conformational sampling insights.

Yes, you need Python because the skill requires OpenMM and MDAnalysis to run MD simulations and analyze biomolecular dynamics. These Python dependencies support the full workflow from system preparation through trajectory analysis.