Return the GROMACS version, build config, binary path, and project root.

List files in a project work directory.

Read a safe text file from a work directory; output is clipped.

Write a safe text MDP/topology-style file into a work directory.

Write a conservative energy-minimisation MDP template.

Write a conservative NVT equilibration MDP template.

Write a conservative NPT equilibration MDP template.

Write a conservative production-MD MDP template.

Validate a text MDP file for syntax and common safety issues.

Build topology and processed coordinates from a PDB/GRO structure.

Define a simulation box around a structure.

Fill a box with solvent and update the topology.

Preprocess MDP, structure, and topology into a TPR run input.

Add counter-ions by replacing solvent molecules.

Post-process a trajectory: PBC treatment, centering, and conversion.

Create or edit a GROMACS index file with gmx make_ndx.

Extract an energy term from an EDR file with gmx energy.

Calculate RMSD with gmx rms.

Calculate residue/atom RMSF with gmx rmsf.

Calculate radius of gyration with gmx gyrate.

Calculate hydrogen bonds with gmx hbond.

Calculate solvent-accessible surface area with gmx sasa.

Check a GROMACS file with gmx check.

Start a simulation in the background and return immediately with a job id.

Check a background simulation and return progress plus log tail.

List all known background simulations and their current status.

Stop a running background simulation with SIGTERM.

Read the captured stdout/stderr log for a background simulation.

Remove finished job records from the registry.

Remove one job record; running jobs require force=True.

Run any non-blocking gmx subcommand not covered by a dedicated tool.