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Found 3 Skills
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.
Comprehensive guide for MDAnalysis - the Python library for analyzing molecular dynamics trajectories. Use for trajectory loading, RMSD/RMSF calculations, distance/angle/dihedral analysis, atom selections, hydrogen bonds, solvent accessible surface area, protein structure analysis, membrane analysis, and integration with Biopython. Essential for MD simulation analysis.
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.