Every study will be reproducible and traceable, and its Config validated before it runs.
MDXplora prepares the system, runs the dynamics, analyses the trajectory and writes up the study, in your browser.
MDXplora is being built and opens to early-access groups in stages. This site describes it as planned.
Simulate trypsin with benzamidine bound at pH 6.5 for 100 ns
systems:
- system: 3PTB
setup:
ph: 6.5
forcefield: amber-openff
ligand_name: BEN
simulation:
duration_ns: 100One file describes the whole study. Four phases run from it, each in its own directory, and one record says what actually happened.
ConfigOne file: the system, how it is prepared, how it is simulated, what is analysed and how it is reported.
setupFetches or reads the structure, repairs what is missing, decides what each non-standard residue is for, then solvates and adds ions.
simulationMinimisation, NVT and NPT equilibration, then production. Restraints, membranes and biased sampling when the study asks for them.
analysisEach analysis works on its own copy of the trajectory and records the settings it actually used.
reportA methods paragraph assembled from recorded values, and a convergence section that says what the trajectory can support.
ManifestEvery phase, artifact and setting, and the software stack it ran on. Readable by someone who was not there.
Say what you want in a sentence. The Agent writes the study’s Config, and MDXplora validates it, as it does every Config, before anything runs.
A form that shows and explains every setting and validates each one as you go, for when you know exactly what you want.
Upload a Config you already have. It runs as written, and every study can be downloaded as a Config again.
Fold, flexibility, secondary structure, native contacts and conformational clustering, from a PDB code. Fluctuations can be set against the crystal’s own B-factors.
The ligand is found, its chemistry resolved and its protonation determined in the binding site. Interactions against published criteria show what holds it, not only what it touches.
Embedded in a lipid bilayer, with its orientation checked rather than assumed and pressure coupling suited to a lipid system.
Umbrella sampling, metadynamics and steered MD from a named collective variable. Each result says what it is and what it is not.
Skip the simulation and analyse trajectories written by other engines, in their own formats.
Mutants against wild type, a sweep across a setting, one run per GPU, and a comparison report across all of them.
An ambiguous ligand charge, a protein backwards in its membrane, a free-energy surface that never converged: each stops the run and is named, not papered over.
Ligand BEN: the study states a net charge of +1, and the chemistry file carries formal charges summing to 0. The file is the chemistry, so the two cannot both stand.
Supply the ligand in the protonation state the study means, then run again.
Studies will run on GPUs we provide. Connecting your own workstation or cluster is planned: your machine will ask MDXplora for work, so nothing reaches into your network.
How your own compute will connectEvery study can be downloaded whole: the Config, the data, the report and the Manifest.
For groups without someone to run molecular dynamics, and for labs that depend on it.
About our servicesYou get the report, the data and the full record behind them.
From a first study to your own campaigns, on your own systems.
For your machines, for studies that refuse, and for results that need a second pair of eyes.
MDXplora is being built and opens to early-access groups in stages, a small number first. Ask for a place through the contact form and we will be in touch as places open.
No. Studies will run on GPUs we provide. Connecting your own workstation or cluster, and choosing for each study where it runs, is planned.
Studies will run on our GPUs and will be stored for your account. Once your own machines can be connected, studies run there will be able to keep their trajectories on your own storage, with only the records and reports shown in MDXplora.
Results produced on MDXplora will be computed with FastMDXplora. Cite the paper it asks to be cited (10.1002/jcc.70350) and the release named in your study’s Manifest (10.5281/zenodo.17510591).