MD Simulation

Overview

This skill drives the FastFold Workflows API to run molecular dynamics simulations, retrieve metrics/plots/CSV plot data, and extract trajectory frames as PDB files.

Current engine:

• CALVADOS + OpenMM (workflow type: calvados_openmm_v1), preset single_af_go (AF structure + PAE).

Flows covered:

1. From an existing fold job (sourceType: fold_job) — auto-resolve structure + PAE.
2. Manual upload — upload PDB and PAE JSON through the Library API, then pass refs in workflow_input.files.
3. From an existing OpenMM workflow — fetch its stored input payload, keep the same input files, set params explicitly, then submit a new workflow.

Both paths end in the same result shape: artifacts list, metrics, and metricsJson inside the latest task's result_raw_json. Completed OpenMM workflows can also extract a specific trajectory conformation with POST /v1/workflows/openmm/<workflow_id>/extract-frame.

Authentication