MD Simulation Suite

Code2Fold Studio

A complete molecular-dynamics workbench in the browser. Prepare a system, pick a force field, launch a simulation, then dive into a rich analysis suite built for real research questions.

12+
Analysis modules
4
Force fields
µs
Trajectory scale
studio · 6VXX_run01
RMSD
1.42 Å
Radius of gyration
18.7 Å
H-bonds
214
Potential E
−4.8e5
Inside Studio

Everything a simulation needs,
in one place

System preparation

Solvate, neutralize, and parametrize in a few clicks — water models, ions, and box geometry handled for you.

Force fields

AMBER ff19SB, CHARMM36m, OPLS-AA and GROMOS — choose the right physics for proteins, lipids, and ligands.

Ensembles & control

NVT / NPT equilibration, thermostats and barostats, with full control over timestep and run length.

Trajectory analytics

RMSD, RMSF, Rg, SASA, hydrogen bonds, and energy terms — computed and plotted automatically.

Essential dynamics

PCA, free-energy landscapes, and conformational clustering reveal the motions that actually matter.

Export & reproduce

Publication-ready figures, CSV metrics, and a full parameter log — every run is reproducible by design.

Analysis library

A diverse suite of MD analyses

From global stability to per-residue detail — the metrics you reach for, ready out of the box.

RMSD over time
RMSF per residue
Radius of gyration
SASA
Hydrogen bonds
Energy terms
Contact map
PCA / ess. dynamics
Free-energy landscape
Ramachandran
Secondary structure
Ligand RMSD & contacts
How it works

Four steps from structure to insight

No installs, no cluster tickets. Studio orchestrates the whole pipeline and surfaces the results as you go.

Continue to Studio →
1

Prepare

Import a PDB/CIF, clean it, solvate, and add ions — your system is simulation-ready in minutes.

2

Simulate

Pick a force field and ensemble, then launch minimization, equilibration, and production runs.

3

Analyze

Explore the full analysis suite with interactive, linked plots and per-residue detail.

4

Export

Download figures, metrics, and a reproducible parameter log to share with your team.

Ready when you are

Open the Studio dashboard

You've seen what's inside — jump into a live, interactive MD analysis workspace.