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GROMACS with Cudo Compute

GROMACS is a molecular dynamics package mainly designed for simulations of proteins, lipids, and nucleic acids. It was originally developed in the Biophysical Chemistry department of University of Groningen, and is now maintained by contributors in universities and research centers worldwide


  • Create a project and add an SSH key
  • Optionally download CLI tool
  • Choose a VM with an NVIDIA GPU and Configure
  • Use the Ubuntu 22.04 + Nvidia drivers + Docker image (in CLI tool type -image ubuntu-nvidia-docker)

Running GROMACS on Cudo Compute with Docker

SSH into your VM and run the following commands

To download the sample benchmark

wget -c${DATA_SET}.tar.gz
tar xf ${DATA_SET}.tar.gz
cd ./water-cut1.0_GMX50_bare/1536
DOCKER="docker run --gpus all -it --rm -v ${PWD}:/host_pwd --workdir /host_pwd
${DOCKER} gmx grompp -f pme.mdp
${DOCKER} gmx mdrun -ntmpi 4 -nb gpu -pin on -v -noconfout -nsteps 5000 -s -ntomp 10

See the GROMACS docs here

Learn more about GROMACS on Cudo Compute

or get started with Cudo Compute.