The four phases

A FastMDXplora study runs as four phases in sequence. Each writes to its own subdirectory under the project output root and records a structured manifest of the parameters, software versions, and artifacts it produced, so every result is traceable to the options that generated it.

  setup  ->  simulation  ->  analysis  ->  report

You can run the whole pipeline at once, or restrict it to specific phases with --include / --exclude (CLI) or the equivalent API arguments.

setup

Prepares a raw structure into a simulation-ready system. PDBFixer repairs the input (missing atoms and residues, protonation at a chosen pH), then the system is solvated in a water box and neutralized with ions. A named force field is selected (CHARMM36 by default; AMBER variants and an OpenFF small-molecule path are available). When a ligand is supplied, it is parameterized with OpenFF and its bound pose is clash-checked before the run proceeds.

Key outputs: prepared.pdb, solvated.pdb, topology.pdb, system.xml, setup_parameters.json.

simulation

Runs molecular dynamics with OpenMM: energy minimization, NVT and NPT equilibration, then production. Integrator, thermostat/barostat, step counts, and reporter intervals are all configurable. Optional PLUMED enhanced sampling (metadynamics, umbrella sampling, steered MD) is applied to the production stage, leaving equilibration unbiased.

Key outputs: production.dcd, state_final.xml, simulation_parameters.json (plus COLVAR, HILLS, plumed.dat when PLUMED is enabled).

analysis

Computes structural and dynamic metrics from the trajectory and renders a figure for each. The standard suite covers RMSD, RMSF, radius of gyration, hydrogen bonds, secondary structure, clustering, dimensionality reduction, Q-value, and dihedrals. When a ligand is present, protein-ligand analyses run automatically: ligand pose RMSD, protein-ligand contacts with a binding-site fingerprint, protein-ligand hydrogen bonds, and ligand RMSF. An analysis scope (solute, protein, ligand, all) controls which atoms each metric considers.

Key outputs: <analysis>/*.dat, <analysis>/*.png, analysis_manifest.json.

report

Assembles the results into shareable deliverables: a structured Markdown report, a slide deck, and a self-contained project bundle.

Key outputs: report.md, slides.pptx, project_bundle.zip.