gromacs — molecular dynamics
GROMACS — a fast, parallel molecular-dynamics simulator. The image is built with CUDA GPU acceleration enabled.
Image tag
docker.io/manvarharsh/gromacs:cuda12
What’s in this image
- Base:
nvidia/cuda:12.4.1-cudnn-devel-ubuntu22.04 - Python 3.10 (conda)
- GROMACS (built with CUDA, installed under
/opt/gromacs) - JupyterHub with Podstack authenticator
- OpenSSH server
Default ports
| Port | Service |
|---|---|
| 22 | SSH |
| 8000 | JupyterHub |
Use cases
- Protein / lipid / membrane MD simulations on GPU
- Free-energy calculations
- Enhanced-sampling methods (REMD, metadynamics via PLUMED if you install it)
- Reproducible computational chemistry pipelines via notebooks
Environment variables
| Variable | Description |
|---|---|
ENABLE_SSH | Enable SSH server |
ENABLE_JUPYTERHUB | Enable JupyterHub on port 8000 |
PODSTACK_API_URL | Backend URL for JupyterHub token validation |
SSH_PUBLIC_KEY | Public key for SSH |
Persistence
Mount at /data. Input topologies in /data/inputs/, trajectory output in /data/output/.