### Extra mdrun Options Example

Source: https://github.com/marrink-lab/shocker/blob/Shocker/README.md

Example of extra mdrun options that can be provided via the -options flag.

```bash
-ntmpi 6
-ntomp 3
-dlb auto
-pin on
-nb gpu
-bonded gpu
```

--------------------------------

### Install Shocker

Source: https://github.com/marrink-lab/shocker/blob/Shocker/README.md

Installs the Shocker package using pip.

```bash
pip install ./
```

--------------------------------

### Bash Script Environment Setup

Source: https://github.com/marrink-lab/shocker/blob/Shocker/README.md

Sets up the environment in a bash script for running Shocker.

```bash
module load 2021
module load Python/3.9.5-GCCcore-10.3.0
source ~/venv/bin/activate
```

--------------------------------

### Hypotonic Osmotic Shock Simulation

Source: https://github.com/marrink-lab/shocker/blob/Shocker/README.md

Example command to initiate a hypotonic osmotic shock simulation.

```bash
shocker -c POPC_ion.gro -f martini_md_anis.mdp -p topol_ion.top -r 200 -e 200 -n index_ion.ndx -shock hypotonic
```

--------------------------------

### Shape Analysis During Hypertonic Shock

Source: https://github.com/marrink-lab/shocker/blob/Shocker/README.md

Example command to perform shape analysis during a hypertonic shock simulation.

```bash
shocker -c POPC_ion.gro -f martini_md_anis_ions.mdp -p topol_ion.top -r 200 -e 200 -n index_ion.ndx -vd yes -i yes
```

--------------------------------

### Hypertonic Shock Simulation Command

Source: https://github.com/marrink-lab/shocker/blob/Shocker/README.md

Example command to run a hypertonic osmotic shock simulation on a vesicle.

```bash
shocker -c POPC_vesicle.gro -f martini_md_anis.mdp -p topol_POPC.top -r 200 -e 200 -n index_POPC.ndx
```

--------------------------------

### Create Virtual Environment

Source: https://github.com/marrink-lab/shocker/blob/Shocker/README.md

Creates a Python virtual environment.

```python3
python3 -m venv venv
```

--------------------------------

### Load Python Module on Snellius

Source: https://github.com/marrink-lab/shocker/blob/Shocker/README.md

Loads the required Python module on the Snellius cluster.

```bash
module load 2021
module load Python/3.9.5-GCCcore-10.3.0
```

--------------------------------

### Clone Repository

Source: https://github.com/marrink-lab/shocker/blob/Shocker/README.md

Clones the Shocker repository from GitHub.

```bash
git clone https://github.com/marrink-lab/shocker
```

=== COMPLETE CONTENT === This response contains all available snippets from this library. No additional content exists. Do not make further requests.