FastMDXplora

Molecular dynamics from a PDB code to a finished study — in one command.

Documentation · Quick start · GUI · Cite

fastmdx explore --system 181L

setup  →  simulation  →  analysis  →  report

Four characters of PDB ID as input. FastMDXplora fetches T4 lysozyme, parameterises the benzene bound in its cavity, runs the dynamics, analyses the trajectory, works out which residues hold the ligand in place, and writes the whole study up as a PDF.

Run all four phases, or any one on its own — fastmdx setup, simulate, analyze, report. Each records what it did, so a run can be picked up, repeated or explained afterwards.

Or open the GUI and watch it happen:

fastmdx gui

Install

conda install -c conda-forge fastmdxplora
fastmdx info

fastmdx info lists every backend and how to get anything missing.

What you can study


A protein on its own	Fold, flexibility, secondary structure, native contacts, conformational clustering — from a PDB code.
A protein with a ligand	The ligand is found, its chemistry resolved, its protonation settled in the binding site. Eight interaction types against published criteria tell you what holds it, not just what it touches.
A membrane protein	Embedded in one of seven bilayers, with the orientation checked rather than assumed and pressure coupling that suits a lipid system.
Free energy along a coordinate	Umbrella sampling, metadynamics and steered MD from a named collective variable — eight of them — without writing PLUMED input. Each says what its output is and is not: a surface if the bias converged, a pathway and the work along it, a potential of mean force if the windows overlap.
A trajectory from another engine	Skip the simulation and analyse what you already have, from anything MDTraj reads.
Many systems at once	Mutants against wild type, a sweep across a setting, runs pinned one per GPU, and a comparison report across all of them.
Water that stays	The positions a water holds through a run, and whether one molecule sat there or a hundred passed through — which are different findings about a binding site.

And where a structure does not say enough — an ambiguous ligand charge, a protein pointed the wrong way for a membrane — FastMDXplora stops and names what it could not decide, rather than returning a number that looks fine.

Every step says why it is happening while it happens, with a citation where there is one worth following, so a first simulation produces a trajectory you can defend rather than one you merely have.

Documentation

Start here — Install · Your first run · The GUI · The four phases

Going further — Restraints, membranes, enhanced sampling · Production and GPUs · Protein-ligand interactions

Reference — CLI · Configuration · Examples · Python API

Citation

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

@article{aina2026fastmd,
  author  = {Aina, Adekunle and Kwan, Derrick},
  title   = {FastMDAnalysis: Software for Automated Analysis of Molecular Dynamics Trajectories},
  journal = {Journal of Computational Chemistry},
  volume  = {47},
  number  = {8},
  pages   = {e70350},
  year    = {2026},
  doi     = {10.1002/jcc.70350},
}

Contributing

Contributions welcome — see CONTRIBUTING.md. FastMDXplora follows the Contributor Covenant.

License

MIT. See LICENSE.

Built in the AAI Research Lab at California State University Dominguez Hills, on MDTraj, OpenMM, PDBFixer, OpenFF, RDKit, NumPy, SciPy, scikit-learn and Matplotlib.

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