PDB2DAT: Automating LAMMPS data file generation from PDB molecular systems using Python, Rdkit, and Pysimm

Pdb2dat, developed in Python, is an open-source, self-contained utility that facilitates the conversion of PDB files into LAMMPS data files, catering to the need of initializing atomistic simulation from initial atomic configurations. It extracts molecular details from PDB files, uses Rdkit and Xyz2mol for bonding analysis and 3D conformer...

SMI2PDB: A self-contained Python tool to generate atomistic systems of organic molecules using their SMILES notations

The advent of computational techniques, particularly atomistic simulations, has lessened the dependency on physical experiments in various scientific fields. Yet, the preparation complexity for simulations using platforms like LAMMPS and GROMACS persists. We introduce SMI2PDB, a Python tool that automates molecular systems assembly from SMILES...

Effect of Bio-oil on Rheology and Chemistry of Organosolv Lignin–Modified Bitumen

Lignin, one of the most abundant natural polymers, has been extensively studied as an additive in bituminous binders. Even though the lignin improves the overall resistance against oxidative aging of bitumen, it could lead to high thermal cracking sensitivity. In this study, a bio-oil (i.e., rapeseed oil) is implemented in lignin-modified...