AA2UA: Converting all-atom models into their united atom coarse grained counterparts for use in LAMMPS. - Eli I. Assaf; Xueyan Liu 014; Sandra Erkens (Softw. Impacts, 2024)

SMI2PDB: A self-contained Python tool to generate atomistic systems of organic molecules using their SMILES notations. - Eli I. Assaf; Xueyan Liu 014; Peng Lin; Sandra Erkens (Softw. Impacts, 2024)

PDB2DAT: Automating LAMMPS data file generation from PDB molecular systems using Python, Rdkit, and Pysimm. - Eli I. Assaf; Xueyan Liu 014; Peng Lin; Sandra Erkens (Softw. Impacts, 2024)

Scymol: A python-based software package for initializing and running molecular dynamics simulations using LAMMPS. - Eli I. Assaf; Elsa Maalouf; Xueyan Liu 014; Peng Lin; Sandra Erkens (SoftwareX, 2025)