Getting Started#

Welcome to BATTER. This short guide provides the key resources new users and developers should consult in order to become productive quickly.

Important

Before submitting jobs through Slurm, make sure the seeded files under ~/.batter/ are edited for your cluster so Amber/AmberTools loads successfully. In practice this usually means updating job_manager.header and SLURMM-Am.header (and SLURMM-BATCH-remd.header if you plan to use REMD) so the right modules, environment activation, and executable paths are set for your site.

If the folder has not been created yet, run batter seed-headers first. If you use a custom header directory, the same requirement applies to the location pointed to by run.slurm_header_dir. See SLURM header templates for the full layout and examples.

If you need to compile or patch AMBER GPU builds for BATTER runs, review AMBER GPU Compilation Notes before launching production windows.

Follow the Tutorial#

The best way to see BATTER in action is to follow Tutorials. It walks through setting up an environment, preparing input files, and running full ABFE and RBFE examples. Completing the tutorial ensures all required dependencies are installed and introduces the core workflow.

Configuration Reference#

For a complete description of the YAML schemas, default values, and validation rules, refer to Configuration Overview. It details every field in RunConfig and SimulationConfig, including advanced options such as restraint overrides, REMD setup, or SLURM-specific controls.

Understanding the outputs#

batter generates several output files and directories during execution. Use Results Folder Layout to inspect the output layout, and consult BATTER Developer Guide when debugging orchestration or analysis internals.

Developing Pipelines#

If you plan to modify or extend BATTER’s internals—for example, adding new pipeline steps or integrating a custom backend—read the BATTER Developer Guide. These documents explain the architecture, typed payloads, metadata model, and orchestration flow used by the codebase.

Additional Resources#

  • examples/ – Ready-to-run YAML configurations demonstrating ABFE (membrane and soluble), RBFE, ASFE, and plain MD scenarios.

  • tests/ – A suite of unit tests that exercise pipeline handlers, state registry, and metadata helpers; useful for understanding expected behaviour.

  • README.rst – Project overview, installation, and quickstart commands.

  • TODO – Current developer to-do list and open enhancements.

  • GitHub Issues / Discussions – Report bugs or request features; link available from the repository homepage.