# Good Research Practice in MD Simulations - TUC/SWZ

## Good Research Practice in MD Simulations - TUC/SWZ

- [Introduction](https://tu-clausthal.gitbook.io/good-research-practice-in-md-simulations-tuc-swz/readme.md): A practical guide for organizing, documenting, and sharing MD simulation research at SWZ and TU Clausthal
- [Motivation](https://tu-clausthal.gitbook.io/good-research-practice-in-md-simulations-tuc-swz/readme/motivation.md): Reproducibility matters most when a project needs to be rerun, checked, or handed to someone else.
- [Contacts](https://tu-clausthal.gitbook.io/good-research-practice-in-md-simulations-tuc-swz/readme/contacts.md)
- [Direct Contact via Matrix/Element](https://tu-clausthal.gitbook.io/good-research-practice-in-md-simulations-tuc-swz/readme/contacts/direct-contact-via-matrix-element.md)
- [Simple Rules](https://tu-clausthal.gitbook.io/good-research-practice-in-md-simulations-tuc-swz/readme/simple-rules.md)
- [Two Phase Approach](https://tu-clausthal.gitbook.io/good-research-practice-in-md-simulations-tuc-swz/readme/two-phase-approach.md)
- [Disclaimer](https://tu-clausthal.gitbook.io/good-research-practice-in-md-simulations-tuc-swz/readme/disclaimer.md)
- [Infrastructures](https://tu-clausthal.gitbook.io/good-research-practice-in-md-simulations-tuc-swz/infrastructures.md)
- [Software Features](https://tu-clausthal.gitbook.io/good-research-practice-in-md-simulations-tuc-swz/infrastructures/software-features.md)
- [Atomsk](https://tu-clausthal.gitbook.io/good-research-practice-in-md-simulations-tuc-swz/infrastructures/software-features/atomsk.md): A tool for building and manipulating atomic systems for MD simulations
- [LAMMPS](https://tu-clausthal.gitbook.io/good-research-practice-in-md-simulations-tuc-swz/infrastructures/software-features/lammps.md)
- [Install](https://tu-clausthal.gitbook.io/good-research-practice-in-md-simulations-tuc-swz/infrastructures/software-features/lammps/install.md)
- [Running LAMMPS](https://tu-clausthal.gitbook.io/good-research-practice-in-md-simulations-tuc-swz/infrastructures/software-features/lammps/running-lammps.md)
- [Automatizing Complex Workflows](https://tu-clausthal.gitbook.io/good-research-practice-in-md-simulations-tuc-swz/infrastructures/software-features/lammps/automatizing-complex-workflows.md)
- [Resources](https://tu-clausthal.gitbook.io/good-research-practice-in-md-simulations-tuc-swz/infrastructures/software-features/lammps/resources.md)
- [OVITO](https://tu-clausthal.gitbook.io/good-research-practice-in-md-simulations-tuc-swz/infrastructures/software-features/ovito.md)
- [Hardware Options](https://tu-clausthal.gitbook.io/good-research-practice-in-md-simulations-tuc-swz/infrastructures/hardware-options.md)
- [Personal PCs/Laptop](https://tu-clausthal.gitbook.io/good-research-practice-in-md-simulations-tuc-swz/infrastructures/hardware-options/personal-pcs-laptop.md)
- [Computing Cluster at TU Clausthal](https://tu-clausthal.gitbook.io/good-research-practice-in-md-simulations-tuc-swz/infrastructures/hardware-options/computing-cluster-at-tu-clausthal.md)
- [HLRN](https://tu-clausthal.gitbook.io/good-research-practice-in-md-simulations-tuc-swz/infrastructures/hardware-options/hlrn.md)
- [Scientific Computing - Leibniz Universität IT Services](https://tu-clausthal.gitbook.io/good-research-practice-in-md-simulations-tuc-swz/infrastructures/hardware-options/scientific-computing-leibniz-universitat-it-services.md)
- [Workflows](https://tu-clausthal.gitbook.io/good-research-practice-in-md-simulations-tuc-swz/workflows.md)
- [Research Design](https://tu-clausthal.gitbook.io/good-research-practice-in-md-simulations-tuc-swz/workflows/research-design.md)
- [Documentation](https://tu-clausthal.gitbook.io/good-research-practice-in-md-simulations-tuc-swz/workflows/documentation.md)
- [Logbook](https://tu-clausthal.gitbook.io/good-research-practice-in-md-simulations-tuc-swz/workflows/documentation/logbook.md): The following guidelines outline the requirements for maintaining a logbook
- [RDM Documentation](https://tu-clausthal.gitbook.io/good-research-practice-in-md-simulations-tuc-swz/workflows/documentation/rdm-documentation.md)
- [eLab Notebooks](https://tu-clausthal.gitbook.io/good-research-practice-in-md-simulations-tuc-swz/workflows/elab-notebooks.md)
- [Methods and Standards](https://tu-clausthal.gitbook.io/good-research-practice-in-md-simulations-tuc-swz/workflows/methods-and-standards.md)
- [Quality Assurance](https://tu-clausthal.gitbook.io/good-research-practice-in-md-simulations-tuc-swz/workflows/methods-and-standards/page-2.md)
- [Providing Public Access to Research Results](https://tu-clausthal.gitbook.io/good-research-practice-in-md-simulations-tuc-swz/workflows/providing-public-access-to-research-results.md)
- [Data Management Plan](https://tu-clausthal.gitbook.io/good-research-practice-in-md-simulations-tuc-swz/data-management-plan.md)
- [Phase 1: Internal](https://tu-clausthal.gitbook.io/good-research-practice-in-md-simulations-tuc-swz/data-management-plan/phase-1-internal.md)
- [Raw Data Storage](https://tu-clausthal.gitbook.io/good-research-practice-in-md-simulations-tuc-swz/data-management-plan/phase-1-internal/raw-data-storage.md)
- [Replication Packages (Internal)](https://tu-clausthal.gitbook.io/good-research-practice-in-md-simulations-tuc-swz/data-management-plan/replication-packages-internal.md)
- [Data Format](https://tu-clausthal.gitbook.io/good-research-practice-in-md-simulations-tuc-swz/data-management-plan/replication-packages-internal/data-format.md)
- [Data Processing](https://tu-clausthal.gitbook.io/good-research-practice-in-md-simulations-tuc-swz/data-management-plan/replication-packages-internal/data-processing.md)
- [Logbook](https://tu-clausthal.gitbook.io/good-research-practice-in-md-simulations-tuc-swz/data-management-plan/replication-packages-internal/logbook.md)
- [Storage and Backup](https://tu-clausthal.gitbook.io/good-research-practice-in-md-simulations-tuc-swz/data-management-plan/replication-packages-internal/storage-and-backup.md)
- [Storage](https://tu-clausthal.gitbook.io/good-research-practice-in-md-simulations-tuc-swz/data-management-plan/replication-packages-internal/storage-and-backup/storage.md)
- [Raw Data Storage](https://tu-clausthal.gitbook.io/good-research-practice-in-md-simulations-tuc-swz/data-management-plan/replication-packages-internal/storage-and-backup/raw-data-storage.md)
- [Acquisition Software and Metadata](https://tu-clausthal.gitbook.io/good-research-practice-in-md-simulations-tuc-swz/data-management-plan/replication-packages-internal/storage-and-backup/acquisition-software-and-metadata.md)
- [Software Features](https://tu-clausthal.gitbook.io/good-research-practice-in-md-simulations-tuc-swz/data-management-plan/replication-packages-internal/software-features.md)
- [LAMMPS](https://tu-clausthal.gitbook.io/good-research-practice-in-md-simulations-tuc-swz/data-management-plan/replication-packages-internal/software-features/lammps.md)
- [Hardware Options](https://tu-clausthal.gitbook.io/good-research-practice-in-md-simulations-tuc-swz/data-management-plan/replication-packages-internal/hardware-options.md)
- [Computing Cluster at TU Clausthal](https://tu-clausthal.gitbook.io/good-research-practice-in-md-simulations-tuc-swz/data-management-plan/replication-packages-internal/hardware-options/computing-cluster-at-tu-clausthal.md)
- [HLRN](https://tu-clausthal.gitbook.io/good-research-practice-in-md-simulations-tuc-swz/data-management-plan/replication-packages-internal/hardware-options/hlrn.md)
- [Hannover Cluster](https://tu-clausthal.gitbook.io/good-research-practice-in-md-simulations-tuc-swz/data-management-plan/replication-packages-internal/hardware-options/hannover-cluster.md)
- [Personal PCs/Laptops](https://tu-clausthal.gitbook.io/good-research-practice-in-md-simulations-tuc-swz/data-management-plan/replication-packages-internal/hardware-options/personal-pcs-laptops.md)
- [Verifiability](https://tu-clausthal.gitbook.io/good-research-practice-in-md-simulations-tuc-swz/data-management-plan/replication-packages-internal/verifiability.md)
- [Possible Implementations](https://tu-clausthal.gitbook.io/good-research-practice-in-md-simulations-tuc-swz/data-management-plan/replication-packages-internal/possible-implementations.md)
- [Pilot](https://tu-clausthal.gitbook.io/good-research-practice-in-md-simulations-tuc-swz/data-management-plan/replication-packages-internal/pilot.md)
- [Phase 2: Open Access](https://tu-clausthal.gitbook.io/good-research-practice-in-md-simulations-tuc-swz/data-management-plan/phase-2-open-access.md)
- [Policies for Open Access Constraints](https://tu-clausthal.gitbook.io/good-research-practice-in-md-simulations-tuc-swz/data-management-plan/policies-for-open-access-constraints.md)
- [Open Access to Data](https://tu-clausthal.gitbook.io/good-research-practice-in-md-simulations-tuc-swz/data-management-plan/open-access-to-data.md)
- [Tools](https://tu-clausthal.gitbook.io/good-research-practice-in-md-simulations-tuc-swz/data-management-plan/tools.md)
- [Pizza.py](https://tu-clausthal.gitbook.io/good-research-practice-in-md-simulations-tuc-swz/data-management-plan/tools/pizza.py.md)
- [Zenodo](https://tu-clausthal.gitbook.io/good-research-practice-in-md-simulations-tuc-swz/data-management-plan/tools/zenodo.md)
- [Best Practices](https://tu-clausthal.gitbook.io/good-research-practice-in-md-simulations-tuc-swz/best-practices.md)
- [Training](https://tu-clausthal.gitbook.io/good-research-practice-in-md-simulations-tuc-swz/best-practices/training.md)
- [NFDI-MatWerk](https://tu-clausthal.gitbook.io/good-research-practice-in-md-simulations-tuc-swz/best-practices/nfdi-matwerk.md)
- [List of Open Access](https://tu-clausthal.gitbook.io/good-research-practice-in-md-simulations-tuc-swz/best-practices/list-of-open-access.md)
- [Publication and Data](https://tu-clausthal.gitbook.io/good-research-practice-in-md-simulations-tuc-swz/best-practices/publication-and-data.md)
- [Contents of a Replication Package](https://tu-clausthal.gitbook.io/good-research-practice-in-md-simulations-tuc-swz/best-practices/publication-and-data/contents-of-a-replication-package.md)
- [Check on Replication Package](https://tu-clausthal.gitbook.io/good-research-practice-in-md-simulations-tuc-swz/best-practices/publication-and-data/check-on-replication-package.md)
- [Securing the Replication Package](https://tu-clausthal.gitbook.io/good-research-practice-in-md-simulations-tuc-swz/best-practices/publication-and-data/securing-the-replication-package.md)
- [Best Practices at Academic Partners](https://tu-clausthal.gitbook.io/good-research-practice-in-md-simulations-tuc-swz/best-practices/best-practices-at-academic-partners.md)
- [Resources](https://tu-clausthal.gitbook.io/good-research-practice-in-md-simulations-tuc-swz/resources.md)
- [Relevant Guidelines](https://tu-clausthal.gitbook.io/good-research-practice-in-md-simulations-tuc-swz/resources/relevant-guidelines.md)
- [Dedicated Solutions](https://tu-clausthal.gitbook.io/good-research-practice-in-md-simulations-tuc-swz/resources/dedicated-solutions.md)
- [TU Clausthal Services](https://tu-clausthal.gitbook.io/good-research-practice-in-md-simulations-tuc-swz/resources/dedicated-solutions/tu-clausthal-services.md)
- [eLabFTW](https://tu-clausthal.gitbook.io/good-research-practice-in-md-simulations-tuc-swz/resources/dedicated-solutions/tu-clausthal-services/elabftw.md)
- [X2Go](https://tu-clausthal.gitbook.io/good-research-practice-in-md-simulations-tuc-swz/resources/dedicated-solutions/tu-clausthal-services/elabftw/x2go.md)
- [Cloud & Storage Service](https://tu-clausthal.gitbook.io/good-research-practice-in-md-simulations-tuc-swz/resources/dedicated-solutions/tu-clausthal-services/cloud-and-storage-service.md)
- [Web Conferences with BigBlueButton (BBB)](https://tu-clausthal.gitbook.io/good-research-practice-in-md-simulations-tuc-swz/resources/dedicated-solutions/tu-clausthal-services/web-conferences-with-bigbluebutton-bbb.md)
- [Research Data Management](https://tu-clausthal.gitbook.io/good-research-practice-in-md-simulations-tuc-swz/resources/dedicated-solutions/tu-clausthal-services/research-data-management.md)
- [GWDG Göttingen Services](https://tu-clausthal.gitbook.io/good-research-practice-in-md-simulations-tuc-swz/resources/dedicated-solutions/gwdg-gottingen-services.md)
- [ShareLaTeX with Overleaf](https://tu-clausthal.gitbook.io/good-research-practice-in-md-simulations-tuc-swz/resources/dedicated-solutions/gwdg-gottingen-services/sharelatex-with-overleaf.md)
- [Code Repository by GitLab](https://tu-clausthal.gitbook.io/good-research-practice-in-md-simulations-tuc-swz/resources/dedicated-solutions/gwdg-gottingen-services/code-repository-by-gitlab.md)
- [URL Shortener](https://tu-clausthal.gitbook.io/good-research-practice-in-md-simulations-tuc-swz/resources/dedicated-solutions/gwdg-gottingen-services/url-shortener.md)
- [Sync Files with ownCloud](https://tu-clausthal.gitbook.io/good-research-practice-in-md-simulations-tuc-swz/resources/dedicated-solutions/gwdg-gottingen-services/sync-files-with-owncloud.md)
- [Glossary](https://tu-clausthal.gitbook.io/good-research-practice-in-md-simulations-tuc-swz/resources/glossary.md)
- [FAQs](https://tu-clausthal.gitbook.io/good-research-practice-in-md-simulations-tuc-swz/resources/faqs.md)