From GROMACS Molecular Dynamics Simulations to Electronic Absorption Spectra: A Tutorial for Small Molecules in Organic Solvents.
- 1Dipartimento di Chimica, Materiali e Ingegneria Chimica "Giulio Natta", Politecnico di Milano, Piazza Leonardo da Vinci, 32-20133 Milano, Italy.
Abstract
Classical molecular dynamics is a theoretical method useful for investigating noncovalent intermolecular interactions and conformational flexibility, enabling the simulation of processes such as aggregation/dissolution and adsorption. Molecular dynamics and quantum chemistry are increasingly introduced in chemistry curricula, yet students may encounter difficulties when translating theoretical concepts into robust simulation protocols, particularly outside biomolecular systems. Here, we present a tutorial designed to guide students through the preparation, execution, and analysis of the simulations of small organic molecules in nonaqueous solvents, followed by the calculation of ultraviolet-visible (UV-vis) absorption spectra using time-dependent density functional theory. This tutorial focuses on several practical issues: obtaining force-field parameters, building simulation cells, selecting ensembles, and interpreting critical simulation parameters. Custom solvent models are validated against reference density and radial distribution functions, demonstrating how selected observables can be used to assess simulation reliability. We illustrate the usefulness of molecular dynamics by showing that molecular flexibility and solvent interactions broaden the UV-vis absorption band of indigo in chloroform. This contribution is intended as a hands-on educational resource for upper-level undergraduate and graduate students enrolled in physical chemistry and computational chemistry courses, as well as for Ph.D. students working in chemistry, physics, or material science, who are approaching molecular simulations. To support dissemination, we have released a ready-to-use package on GitHub that includes solvent boxes and all the necessary files and data for incorporating new molecules into GROMACS simulations: https://github.com/cippee/SolventSafari-for-GROMACS.
Related
- Quantum--classical break-even in electronic dynamics of macrocyclic molecules
- Electronic Density versus Geometry for Machine-Learned Molecular Absorption Spectra
- Thermo-elastic properties of hydrated epoxy-graphene nanocomposites from ensemble-based molecular dynamics simulations
- Molecular dynamics simulations of DMSO-MeOH liquid mixtures. Effects of force fields on mixing properties
- Full molecular dynamics simulations of a single trapped ion in a neutral bath
BibTeX
@article{picarelli2026from,
title = {{From GROMACS Molecular Dynamics Simulations to Electronic Absorption Spectra: A Tutorial for Small Molecules in Organic Solvents.}},
author = {Chiara Picarelli and Giuseppina Raffaini and Matteo Tommasini},
journal = {Journal of chemical education},
year = {2026},
month = sep,
doi = {10.1021/acs.jchemed.6c00154},
url = {https://europepmc.org/article/MED/42899299},
note = {CC BY},
}
RIS
TY - JOUR
TI - From GROMACS Molecular Dynamics Simulations to Electronic Absorption Spectra: A Tutorial for Small Molecules in Organic Solvents.
AU - Chiara Picarelli
AU - Giuseppina Raffaini
AU - Matteo Tommasini
PY - 2026
DA - 2026/09/01
JO - Journal of chemical education
DO - 10.1021/acs.jchemed.6c00154
UR - https://europepmc.org/article/MED/42899299
AB - Classical molecular dynamics is a theoretical method useful for investigating noncovalent intermolecular interactions and conformational flexibility, enabling the simulation of processes such as aggregation/dissolution and adsorption. Molecular dynamics and quantum chemistry are increasingly introduced in chemistry curricula, yet students may encounter difficulties when translating theoretical concepts into robust simulation protocols, particularly outside biomolecular systems. Here, we present a tutorial designed to guide students through the preparation, execution, and analysis of the simulations of small organic molecules in nonaqueous solvents, followed by the calculation of ultraviolet-visible (UV-vis) absorption spectra using time-dependent density functional theory. This tutorial focuses on several practical issues: obtaining force-field parameters, building simulation cells, selecting ensembles, and interpreting critical simulation parameters. Custom solvent models are validated against reference density and radial distribution functions, demonstrating how selected observables can be used to assess simulation reliability. We illustrate the usefulness of molecular dynamics by showing that molecular flexibility and solvent interactions broaden the UV-vis absorption band of indigo in chloroform. This contribution is intended as a hands-on educational resource for upper-level undergraduate and graduate students enrolled in physical chemistry and computational chemistry courses, as well as for Ph.D. students working in chemistry, physics, or material science, who are approaching molecular simulations. To support dissemination, we have released a ready-to-use package on GitHub that includes solvent boxes and all the necessary files and data for incorporating new molecules into GROMACS simulations: https://github.com/cippee/SolventSafari-for-GROMACS.
SN - 0021-9584
ER -