Introduction

Welcome to the MolSysMT User Guide. This section is your starting point if you have just discovered the library and want to understand what it can do for you, how it thinks about molecular systems, and how to get productive quickly.

We suggest the following path if you are new:

• Start with “What is MolSysMT?” to get a high-level overview and see what kinds of problems it can help you solve.

• Follow with “Installation” to get a working setup on your machine.

• Then visit “First steps” for pointers to the Quickstart guide in the Showcase section and a few recommended examples and recipes. We strongly encourage you to complete at least the Quickstart before diving into the more detailed conceptual pages below.

• Once you are comfortable running a few simple examples, visit “Molecular systems” and “Native forms” to learn how MolSysMT represents systems internally and which forms it understands.

• Read “Selection language and syntax” and “Quantities and units” to learn how to select parts of a system and how physical quantities are handled (coordinates, box, time, charges).

• When you are ready to dive deeper, “Overview of tools”, “Viewers and visualization”, and “Supported forms and libraries” show you the main operations and how MolSysMT connects to other packages.

• Next, “Configuration options”, “Memory management”, and “Logging and diagnostics” cover advanced topics that help you tune performance, control output, and debug workflows.

• Finally, “Demo systems” describes the library of pre-bundled molecular systems used throughout the documentation and testing suite, so you know which reference systems appear in examples and tests.

Feel free to jump directly to the section that best matches your current needs, and come back here whenever you want to explore the bigger picture.