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

# Gromacs

> Gromacs is a molecular dynamics package used for researching biological molecular systems.

<img src="https://mintcdn.com/gpuhub/r1V0ko0l9sh4RwWM/images/logo-gromacs.png?fit=max&auto=format&n=r1V0ko0l9sh4RwWM&q=85&s=dd3f1802b279a584e52d168591834908" alt="" width="253" height="64" data-path="images/logo-gromacs.png" />

When creating an instance on GPUhuband selecting the image, use the Gromacs image to create an instance that comes with the Gromacs software package pre-installed. The pre-installed Gromacs has been compiled with CUDA, so it will use GPU acceleration for computations by default.

Here is a test case for Gromacs ([source of the case](https://confluence.csuc.cat/display/HPCKB/How+to+run+a+Gromacs+simulation+of+a+protein)):

## Step 1: Preparation

Create a directory named `test` and navigate into it.

```bash bash theme={null}
mkdir test && cd test
```

## Step 2: Generate Input Files

Run this command separately; otherwise, it may hang. When prompted, select 14: GROMOS96 54a7 and 1: SPC.

```bash bash theme={null}
gmx pdb2gmx -f 2n6m.pdb -o esculentin.gro -p esculentin.top -ignh
```

## Step 3: Set Simulation Parameters

```bash bash theme={null}
gmx editconf -f esculentin.gro -o esculenbox.gro -box 5 5 5
gmx solvate -cp esculenbox.gro -o solvated.gro -p esculentin.top
```

## Step 4: Configuration

Create a configuration file `options.mdp` with the following content:

```bash bash theme={null}
cat > options.mdp << EOF
integrator        = md
nsteps            = 50000000
nstxout           = 50000
coulombtype       = PME
fourierspacing    = 0.15
tcoupl            = v-rescale
tau-t             = 0.2 0.2
ref-t             = 298.15 298.15
tc-grps           = Protein Non-protein
pcoupl            = berendsen
compressibility   = 4.5e-5
tau-p             = 0.2
ref-p             = 1.0
EOF
gmx grompp -f options.mdp -c solvated.gro -p esculentin.top -o esculentin.tpr -maxwarn 100
```

## Step 5: Run Simulation

```bash bash theme={null}
gmx mdrun -s esculentin.tpr
```

## Gromacs Installation Script:

```bash bash theme={null}
wget https://ftp.gromacs.org/gromacs/gromacs-2022.2.tar.gz \
    && tar xfz gromacs-2022.2.tar.gz \
    && cd gromacs-2022.2 \
    && mkdir build \
    && cd build \
    && /root/miniconda3/bin/cmake .. -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON -DGMX_GPU=CUDA -DCUDA_TOOLKIT_ROOT_DIR=/usr/local/cuda \
    && make -j8 && make check && make install \
    && cd ../../ && rm -rf gromacs-* \
    && echo "PATH=/usr/local/gromacs/bin/:\$PATH" >> /etc/profile
```