FastMDXplora documentation

Fully Automated SysTem for Molecular Dynamics eXploration

FastMDXplora explores a protein’s behavior end to end from a single command. Given a structure (or just a PDB ID) it performs molecular dynamics exploration all the way through setup, simulation, analysis, and reporting, then hands back publication-ready results.

Getting started

• Installation
  • Full install (all four phases)
  • Analysis and report only (from PyPI)
  • Verifying the install
• The four phases
  • setup
  • simulation
  • analysis
  • report
• FastMDXplora usage examples
  • Command-line interface
  • Config file format
  • Python API
  • Cross-run comparison report
  • Reproducibility
• Configuration
  • Structure
  • Protein-ligand studies
  • Reproducing a study
  • Full field reference

Reference

• API reference
  • FastMDXplora
  • AnalysisOrchestrator
  • Package metadata

Quick links

• GitHub repository

• PyPI: fastmdxplora

• PyPI: fastmdx (alias)

• Foundational paper (JCC 2026)

Citation

If you use FastMDXplora in your work, please cite:

Aina, A.; Kwan, D. FastMDAnalysis: Software for Automated Analysis of Molecular Dynamics Trajectories. J. Comput. Chem. 2026, 47, e70350. DOI: 10.1002/jcc.70350