> ## Documentation Index
> Fetch the complete documentation index at: https://docs.cudocompute.com/llms.txt
> Use this file to discover all available pages before exploring further.

# GROMACS

> Learn how to utilize GROMACS with the CUDO Compute platform.

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](/docs/tutorials/how-to-generate-ssh-keys)
* Optionally download [CLI tool](/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

```shell theme={null}
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
```

```shell theme={null}
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](https://manual.gromacs.org/documentation/)