v2.4 · invite only Molecular Dynamics — Cloud-Native

The platform
for molecular
simulations.

Build molecular systems, run cloud simulations, analyze trajectories, and share workflows — every step in one place. Zero setup, browser-native.

Request access See the workflow ↳ ~10 min from molecule to running job
LOADING TRAJECTORY…
10×
Faster setup · minutes, not weeks
0
Infrastructure to manage · you write science, we run it
⌬
Marketplace · share structures, force fields, protocols
∑
One platform · build, simulate, analyze, share
§02 · WHY JUNGULAR

Focus on the science, not
the infrastructure.

We took the parts of molecular dynamics that researchers hate — cluster provisioning, engine compilation, file-format wrangling — and made them disappear.

01

Faster setup

From molecule to running job in minutes. No cluster provisioning, no engine compilation, no file-format wrangling.

02

Phase protocols

Define complex multi-phase simulation workflows visually. Checkpointing means your progress survives any interruption.

03

One platform

Build, simulate, analyze, and share. Force fields, protocols, and results — all in one place with a built-in marketplace.

§03 · THE WORKFLOW

Built for molecular
dynamics.

Every step of the workflow, handled — from drawing the first molecule to publishing the final trajectory.

[ 01 ] Build

Visual molecule builder.

Design molecular systems directly in the browser. Draw molecules, import structures, and pack simulation boxes — all without touching the command line.

  • SMILES & PDB import
  • Polymer builder with repeat units
  • Monte Carlo box packing
See it in action
jungular ▸ workspace ▸ polymer-solvent.box geometry · packed
LOADING STRUCTURE…
FIG. 1.1 Real-time visual workspace — drag to rotate the packed polymer/solvent system (170 × 170 × 170 Å). § build.builder
jungular ▸ jobs ▸ polymer-eq-v3 running · 4 / 19 phases
JOB · 8e6e3a0d ⚡ SIMULATING
Polymer Equilibration
52.5 ns · 8 cores · ~13.5 hrs remaining
01NPT300 ps
02NVT3.0 ns
03NPT3.0 ns
04NPT3.0 ns
05NPT3.0 ns
06NPT20 ns
T 298 K P 1.0 atm E_pot -42,180 kcal/mol Δt 1 fs
FIG. 1.2 Multi-phase NPT/NVT protocol editor — 19 phases over 52.5 ns of simulated time. § simulate.protocol
[ 02 ] Simulate

Cloud-native simulations.

Define multi-phase protocols visually — NPT equilibration, temperature ramps, production runs. Submit to the cloud and monitor everything in real time.

  • Visual multi-phase protocol editor
  • Auto-checkpoint & resume on interruption
  • Live energy, temperature & pressure monitoring
Submit your first job
[ 03 ] Analyze

Analyze results in-place.

Explore trajectories with the built-in 3D viewer, run Python notebooks, and build interactive plots — all within the platform, no data export required.

  • 3D trajectory visualization
  • Built-in Jupyter notebooks & CLI
  • Drag-and-drop interactive plotting
Learn more
jungular ▸ analyze ▸ notebook python · ready
3D Viewer
Notebook 1
+ new
[1] python · run with ⌘↵ 
# Compute the O–O radial distribution
import jungular
rdf = jungular.compute_rdf("O", "O", bins=200)
jungular.plot(rdf, title="O-O RDF")
→ Peak at 2.76 Å · n_pairs = 18,432
O–O RDF · g(r)
FIG. 1.3 Radial distribution function g(r) plotted with the native Jungular notebook. § analyze.notebook
jungular ▸ marketplace ▸ force fields community-shared
⌕ Search force fields, protocols, structures…
FF
Dreiding
GENERIC · HYBRIDIZATION-DEPENDENT · BY JUNGULAR
FREE
↓ 2,418
FF
TraPPE-UA
UNITED-ATOM · PHASE EQUILIBRIA · BY JUNGULAR
FREE
↓ 1,062
FF
PCFF
POLYMER · CLASS 2 QUARTIC · BY JUNGULAR
FREE
↓ 980
PR
PMMA quench 600→300K
PROTOCOL · 19 PHASES · BY @nmorgan
12 CR
↓ 184
FIG. 1.4 Community-shared force fields and protocols. Peer-reviewable. § share.marketplace
[ 04 ] Share

A marketplace for science.

Share structures, force fields, and simulation protocols with the community. Publish for free or earn credits when other researchers download your work.

  • Publish structures & force fields
  • Share complete simulation protocols
  • Earn credits from downloads
Browse marketplace
§04 · PROCEDURE

From molecule
to insight.

No DevOps, no compiling, no babysitting clusters. Three steps, one browser tab.

STEP 01 — DESIGN

Design

Draw or import molecules, assign force fields, and pack your simulation box visually.

STEP 02 — SIMULATE

Simulate

Submit to AWS cloud compute. Monitor energy, temperature, and pressure in real time.

STEP 03 — ANALYZE

Analyze

Explore trajectories with Python notebooks and interactive visualization tools.

Ready to accelerate
your research?

Jungular is currently invite-only. Tell us about your work and we'll get you on board.

Request access Read the docs