molecular-dynamics

Run molecular dynamics simulations for protein stability by executing the command with OpenMM and specifying a force field like AMBER14 along with your protein PDB file. The Skill handles system preparation, energy minimization, and equilibration automatically.

Molecular dynamics trajectory analysis with MDAnalysis includes calculating RMSD, RMSF, contact maps, and free energy surfaces. These metrics help study conformational changes, protein-protein interactions, and drug binding events.

You can simulate small molecules, nucleic acids, and membranes in addition to proteins. The Skill provides predefined force field configurations for these molecule types to support diverse biophysics and structural biology workflows.

Molecular dynamics trajectory visualization is supported optionally through NGLView. While OpenMM and MDAnalysis handle the core simulation and analysis, NGLView integrates to provide visual representation of the molecular systems.

Biophysics simulations for drug binding use predefined force field configurations, explicitly including AMBER14. These force fields parameterize proteins, small molecules, membranes, and nucleic acids for accurate molecular dynamics calculations.

OpenMM and MDAnalysis are required dependencies to run molecular dynamics simulations and analyze trajectories. NGLView is an optional dependency needed only if you want to visualize the molecular systems during your workflow.