SMI2PDB

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

Journal Article (2024)
Author(s)

Eli I. Assaf (TU Delft - Pavement Engineering)

X. Liu (TU Delft - Pavement Engineering)

P. Lin (TU Delft - Pavement Engineering, Rijkswaterstaat)

Sandra M.J.G. Erkens (TU Delft - Pavement Engineering, Rijkswaterstaat)

Research Group
Pavement Engineering
DOI related publication
https://doi.org/10.1016/j.simpa.2024.100655
More Info
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Publication Year
2024
Language
English
Research Group
Pavement Engineering
Volume number
20
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Abstract

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 to PDB format, easing molecular dynamics simulation setups. SMI2PDB manages molecule configuration and quantification effortlessly, establishes stable conformers, applies random rotations, and positions them in a simulation box with a Sobol sequence to reduce overlaps. This script facilitates the rapid preparation of complex organic mixtures for use in simulations, enhancing the exploration of novel materials.