Jul 2026· Journal of Chemical Information and Modeling· Vol 66, pp. 8698 - 8704· 0 citations· 50 references
MedicineComputer Science
TL;DR
The versatility of the lmp2gro tool is demonstrated through two case studies: H2 adsorption in MOF-5 (IRMOF-1) using the universal force field (UFF) and the behavior of a water droplet on a silica Q4 surface using the INTERFACE-FF.
Abstract
lmp2gro is a Python utility designed to streamline the generation of GROMACS topologies for systems where traditional parametrization is often challenging. Although developed primarily for periodic systems, such as metal–organic frameworks (MOFs), the tool is equally applicable to molecular systems containing a single residue type. The program parses LAMMPS data files, maps force field terms onto the corresponding GROMACS functional forms, and automatically generates all necessary input files. This workflow enables seamless access to all of the capabilities of the GROMACS simulation engine. The versatility of the tool is demonstrated through two case studies: (i) H2 adsorption in MOF-5 (IRMOF-1) using the universal force field (UFF) and (ii) the behavior of a water droplet on a silica Q4 surface using the INTERFACE-FF. A step-by-step guide is provided for both applications. The lmp2gro source code and tutorial materials are freely available at https://github.com/AlexandreMoniPereira/lmp2gro.
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