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lmp2gro: A Python Tool for Converting LAMMPS Data Files into GROMACS Topologies
Alexandre Moni Pereira1, Jarede da Silva Martins1, Marcelo Albuquerque1
1MolMod-CS, Institute of Chemistry, Fluminense Federal University, Campus Valonguinho, Centro, Niterói-RJ CEP 24020-141, Brazil.
Journal of Chemical Information and Modeling
|July 20, 2026
Summary
The lmp2gro Python utility simplifies generating GROMACS topologies for complex systems like metal-organic frameworks (MOFs). It converts LAMMPS data files, enabling GROMACS simulations for challenging molecular and periodic systems.
Area of Science:
- Computational chemistry
- Materials science
- Molecular dynamics simulations
Background:
- Parametrizing complex molecular systems for simulations can be challenging.
- Traditional methods often struggle with periodic systems like metal-organic frameworks (MOFs).
Purpose of the Study:
- To introduce lmp2gro, a Python utility for automating GROMACS topology generation.
- To facilitate simulations of challenging systems using GROMACS.
Main Methods:
- The lmp2gro tool parses LAMMPS data files.
- It maps force field terms to GROMACS functional forms.
- Automatic generation of GROMACS input files.
Main Results:
- Successfully demonstrated for H2 adsorption in MOF-5 (IRMOF-1) using UFF.
- Showcased utility for simulating water droplet behavior on silica (Q4) with INTERFACE-FF.
- Provides a streamlined workflow for GROMACS simulations.
Conclusions:
- lmp2gro simplifies the creation of GROMACS topologies for diverse systems.
- The tool enhances accessibility to GROMACS simulation capabilities.
- It serves as a valuable resource for computational studies involving MOFs and molecular systems.
