minimize_and_write_pdb

minimize_and_write_pdb(conf_gro: Path, topology: Path, minim_mdp: Path, workdir: Path) → Path

Run an energy minimization workflow and write a minimized PDB file.

This function performs a minimal GROMACS preprocessing and execution pipeline starting from an existing GRO structure. The workflow defines a simulation box, preprocesses inputs, runs an energy minimization, and converts the minimized structure to PDB format.

The workflow assumes that topology generation (e.g. via pdb2gmx) has already been performed.

Parameters:

  • conf_gro (pathlib.Path) – Input GRO structure file.

  • topology (pathlib.Path) – GROMACS topology file.

  • minim_mdp (pathlib.Path) – Energy minimization MDP parameter file.

  • workdir (pathlib.Path) – Working directory used for all intermediate and output files.

Returns:

Path to the minimized PDB file.

Return type:

pathlib.Path