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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
lmp2gro is a Python utility that simplifies GROMACS topology generation for challenging systems like metal-organic frameworks (MOFs). It converts LAMMPS data files to GROMACS input, enabling advanced simulations.
Area of Science:
- Computational Chemistry
- Materials Science
- Molecular Dynamics
Background:
- Parametrizing complex systems for molecular simulations, particularly periodic structures like MOFs, presents significant challenges.
- Existing tools often lack the flexibility to handle diverse force field types and system architectures.
Purpose of the Study:
- To introduce lmp2gro, a Python utility designed to automate and streamline the generation of GROMACS topologies from LAMMPS data files.
- To provide a versatile tool applicable to both periodic systems (e.g., MOFs) and single-residue molecular systems.
Main Methods:
- The lmp2gro utility parses LAMMPS data files, identifying and mapping force field parameters.
- It translates these parameters into the corresponding GROMACS functional forms.
- The tool automatically generates all required GROMACS input files for simulation.
Main Results:
- Successful demonstration of lmp2gro's versatility through two distinct case studies: H2 adsorption in MOF-5 and water droplet behavior on silica.
- Validation of the generated topologies for use with the GROMACS simulation engine.
Conclusions:
- lmp2gro significantly simplifies the process of generating GROMACS topologies for complex systems.
- The tool enhances accessibility to GROMACS capabilities for researchers working with MOFs and other challenging molecular systems.
