Glossary

• MD Simulations: Molecular Dynamics (MD) simulations are computational methods used to study the behavior and interactions of atoms and molecules over time.

• LAMMPS: Large-scale Atomic/Molecular Massively Parallel Simulator (LAMMPS) is a widely-used software package for performing MD simulations.

• Replication Packages: Replication packages contain the data, code, and documentation necessary to reproduce research findings.

• Good Research Practice: Good Research Practice refers to the ethical and methodological standards followed by researchers to ensure the integrity, reproducibility, and reliability of their work.

• Transparency: Transparency in research refers to the openness and accessibility of research methods, data, and findings to facilitate scrutiny, verification, and replication by others.

• Reproducibility: Reproducibility is the ability of researchers to replicate the results of a study using the same methods, data, and analysis procedures.

• Open Science: Open Science promotes the sharing of research outputs, including data, code, and publications, to enhance collaboration, transparency, and innovation in scientific research.

• Metadata: Metadata refers to descriptive information about data, including its origin, structure, format, and other attributes, to facilitate understanding and interpretation.

• Data Management Plan (DMP): A Data Management Plan is a formal document outlining how research data will be collected, stored, managed, and shared throughout the research lifecycle.

• Version Control: Version control is a system that tracks changes to files and documents, allowing researchers to manage and document revisions over time.

• Open Access: Open Access refers to the unrestricted access to research outputs, such as publications and data, allowing anyone to freely access, use, and distribute the information.

• Metadata: Metadata is descriptive information about data, including its origin, structure, format, and other attributes, to facilitate understanding and interpretation.

• Open Innovation: Open Innovation is a collaborative approach to innovation that involves sharing ideas, resources, and knowledge across organizational boundaries to accelerate progress and solve complex problems.

• IP Protection: Intellectual Property (IP) Protection refers to legal mechanisms, such as patents, copyrights, and trademarks, used to protect the rights of creators and owners of intellectual property.

• Force Field: A force field is a mathematical model used in molecular dynamics simulations to describe the interactions between atoms and molecules based on empirical or theoretical principles.

• Analysis Script: An analysis script is a program or script used to analyze data generated from molecular dynamics simulations, such as calculating properties, performing statistical analysis, and visualizing results.

• Best Practices: Best practices refer to established methods, techniques, and procedures that are recognized as effective and efficient for achieving specific goals or objectives in scientific research.

• Data Integrity: Data integrity refers to the accuracy, consistency, and reliability of data throughout its lifecycle, ensuring that data remains valid and trustworthy for analysis and interpretation.

• Data Sharing: Data sharing is the practice of making research data openly available to other researchers, facilitating collaboration, verification, and reuse of data for further research.

• Data Publication: Data publication involves formally documenting and disseminating research data, often in conjunction with a publication or as a standalone dataset, to make it accessible and citable for other researchers.

• Metadata Standard: A metadata standard is a set of guidelines or specifications for describing and organizing metadata associated with research data, ensuring consistency and interoperability across datasets.

• Data Repository: A data repository is a digital platform or service that provides storage, access, and preservation for research data, enabling long-term archiving and sharing of datasets with the research community.