# Introduction

## About this guide

This guide was written and is maintained by Dr.-Ing. Hoang-Thien Luu for Molecular Dynamics work at the Simulation Science Centre Clausthal/Gottingen (SWZ) and TU Clausthal. It is meant as a practical working document for researchers who need a clear way to organize simulations, analysis, documentation, and handover inside the group.

This guide is for researchers at the Simulation Science Centre Clausthal/Gottingen (SWZ) and related groups at TU Clausthal who work with Molecular Dynamics simulations. It brings together the local rules, tools, and habits that make it easier to run projects in a way that is understandable to colleagues, easier to continue after a break, and easier to publish with confidence.

Most of the problems this guide addresses are ordinary ones. Files end up spread across laptops, NAS folders, and cluster home directories. Simulation inputs evolve over time, but the exact version used for a figure is no longer obvious. Analysis scripts work for the original author but are hard for someone else to rerun. When a paper is finished, assembling the data, code, and documentation into a usable replication package takes longer than expected. None of this is unusual, but all of it becomes easier if the project is organized from the beginning.

The pages that follow are meant to help with that day-to-day work. They explain how to structure projects, document runs, keep track of software and hardware, use the SWZ cluster and national HPC systems, and prepare material for internal review or open publication. The goal is not to impose paperwork for its own sake. The goal is to make simulation work easier to check, easier to reuse, and easier to hand over to the next person who needs to understand it.