Molecular Dynamics Docker Images

Common requirements

Install Docker or equivalent container system

For example:

Docker Engine for Debian: https://docs.docker.com/engine/install/debian/

Or Docker Desktop for Windows: https://docs.docker.com/desktop/setup/install/windows-install/

Install Nvidia Container Toolkit (for GPU access)

Docker Desktop for Windows already has the required software. Other than ensuring your GPU drivers are up to date, nothing else is needed.

NCT for Linux: https://docs.nvidia.com/datacenter/cloud-native/container-toolkit/latest/install-guide.html

Clone repo

git clone https://github.com/David-Moody/MDDockerImages.git

Amber

Current version: Amber24

Download required source files

Download AmberTools24 via Option 2: https://ambermd.org/GetAmber.php#ambertools

Download Amber24: https://ambermd.org/GetAmber.php#amber

This has a licensing agreement that you must meet. Including a license fee for commercial use.

Place Amber24.tar.bz2 and AmberTools24.tar.bz2 into Amber folder.

Build the container

cd Amber
docker build . -t amber-cuda:v1
# Run the tests
docker run --gpus=all -it amber-cuda:v1 make test.cuda.serial -j12

Using the container

Change to the directory with your project files for Amber

docker run --gpus=all -it --rm -v .:/data amber-cuda:v1 <AMBER COMMAND>

For example:

docker run --gpus=all -it --rm -v .:/data amber-cuda:v1 cpptraj

OR

docker run --gpus=all -it --rm -v .:/data amber-cuda:v1 /data/dynamics.sh

GROMACS

Current version: 2025.1

cd GROMACS
docker build . -t gromacs:2025.1

Running GROMACS

docker run --gpus=all -it --rm gromacs:2025.1 gmx

With the current working directory bind mounted (like a symbolic link) to /data inside the container.

docker run --gpus=all -it --rm -v .:/data gromacs:2025.1 gmx

Options to consider adding

-DGMX_SIMD=xxx to specify the level of SIMD support of the node on which GROMACS will run

OpenMM

Current version: Always latest

cd OpenMM
docker build . -t openmm:latest

Running OpenMM

docker run --gpus=all -it --rm openmm:latest

With the current working directory bind mounted (like a symbolic link) to /data inside the container.

docker run --gpus=all -it --rm -v .:/data openmm:latest python script.py