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Found 3 Skills
Run OpenMMDL molecular dynamics workflows via the FastFold Workflows API (`openmmdl_v1`) from local topology + optional ligand files, prepare draft scripts, execute drafts, wait for completion, fetch artifacts/metrics, and extract trajectory frames. Use when users ask for OpenMMDL, protein-ligand MD, OpenMMDL script preparation, or `/openmmdl/results/<workflow_id>` reruns.
Run and analyze molecular dynamics simulations with OpenMM and MDAnalysis. Set up protein/small molecule systems, define force fields, run energy minimization and production MD, analyze trajectories (RMSD, RMSF, contact maps, free energy surfaces). For structural biology, drug binding, and biophysics.
Run molecular dynamics (MD) simulations via the FastFold Workflows API. Today supports the CALVADOS+OpenMM workflow (calvados_openmm_v1) from either an existing fold job (AF structure + PAE auto-resolved) or manual PDB+PAE upload, then waits for completion, fetches metrics/plots/CSV artifacts, and extracts trajectory frames as PDB files. Use when running an MD simulation with FastFold, CALVADOS + OpenMM, reading MD metrics/plots, extracting frames, or scripting submit → wait → results for an MD run.