SMI2PDB

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

Journal article (2024)

Authors

E.I. Assaf Martinez-Streignard Pavement Engineering - CEG
X. Liu Pavement Engineering - CEG
P. Lin Pavement Engineering - CEG , Rijkswaterstaat
S. Erkens Pavement Engineering - CEG , Rijkswaterstaat
Research Group
Pavement Engineering (CEG) (TU Delft)
Molecular dynamics Chemistry LAMMPS Atomistic simulation
More Info
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Published Date

2024

Language

English

Faculty

Civil Engineering & Geosciences

Department

Engineering Structures

Research Group

Pavement Engineering

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.