GROMACS - 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

Prerequisites

Create a project and add an SSH key
Optionally download CLI tool
Choose a virtual machine 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 virtual machine and run the following commands To download the sample benchmark

DATA_SET=water_GMX50_bare
wget -c https://ftp.gromacs.org/pub/benchmarks/${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 nvcr.io/hpc/gromacs:2022.1
${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