grompp

Grompp, short for GROMACS preprocessor, is a utility in the GROMACS molecular dynamics package. It prepares the binary run input file, typically with a .tpr extension, from a system’s structure, topology, and simulation parameters. The program validates and integrates information from a coordinate file (such as .gro or .pdb), a topology file describing molecules, bonds, and force fields, and an mdp file containing simulation settings (time step, temperature and pressure control, constraints, PME, etc.). It checks for consistency among files, resolves constraints, and ensures that all required data are present for the chosen simulation.

Grompp then assembles a self-contained run input file that encapsulates coordinates, topology, and run parameters needed by the MD engine. The resulting .tpr file can be used directly by mdrun to execute the simulation. Users can control its behavior with options such as -maxwarn to permit a specified number of non-critical warnings, and -v for verbose output; -po can be used to write modified mdp options to a file.

Typical workflow involves preparing a system with a coordinate file and topology, creating an mdp file with the desired simulation settings, running grompp to generate the .tpr, and then running mdrun -s topol.tpr to start the simulation. Grompp thus serves as the preprocessing step that validates and consolidates inputs into a portable, executable run file for molecular dynamics simulations in GROMACS.