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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\u2013visible (UV\u2013vis) 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\u2013vis 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.<\/jats:p>","DOI":"10.1021\/acs.jchemed.6c00154","type":"journal-article","created":{"date-parts":[[2026,9,3]],"date-time":"2026-09-03T10:18:22Z","timestamp":1788430702000},"page":"5441-5454","source":"Crossref","is-referenced-by-count":0,"title":["From GROMACS\nMolecular Dynamics Simulations to Electronic\nAbsorption Spectra: A Tutorial for Small Molecules in Organic Solvents"],"prefix":"10.1021","volume":"103","author":[{"ORCID":"https:\/\/orcid.org\/0009-0002-5367-8838","authenticated-orcid":true,"given":"Chiara","family":"Picarelli","sequence":"first","affiliation":[{"name":"Piazza Leonardo da Vinci , , ,","place":["Milano, Italy, 32\u221220133"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3462-6514","authenticated-orcid":true,"given":"Giuseppina","family":"Raffaini","sequence":"additional","affiliation":[{"name":"Piazza Leonardo da Vinci , , ,","place":["Milano, Italy, 32\u221220133"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7917-426X","authenticated-orcid":true,"given":"Matteo","family":"Tommasini","sequence":"additional","affiliation":[{"name":"Piazza Leonardo da Vinci , , ,","place":["Milano, Italy, 32\u221220133"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"316","published-online":{"date-parts":[[2026,9,1]]},"reference":[{"key":"2026101310104024000_cit1","doi-asserted-by":"publisher","first-page":"122841","DOI":"10.1016\/j.molliq.2023.122841","article-title":"Curcumin\/Amphiphilic\nCyclodextrin Nanoassemblies: Theoretical and Spectroscopic Studies\nto Address Their Debut in Anticancer Therapy","volume":"389","author":"Zagami","year":"2023","journal-title":"J. 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Soc."},{"issue":"10","key":"2026101310104024000_cit4","doi-asserted-by":"publisher","first-page":"1147","DOI":"10.1248\/bpb.23.1147","article-title":"NMR Structure\nof Ribonuclease HI from Escherichia Coli","volume":"23","author":"Fujiwara","year":"2000","journal-title":"Biol.\nPharm. Bull."},{"issue":"3","key":"2026101310104024000_cit5","doi-asserted-by":"publisher","first-page":"965","DOI":"10.1021\/acs.jctc.2c01044","article-title":"Machine Learning Exciton Hamiltonians\nin Light-Harvesting Complexes","volume":"19","author":"Cignoni","year":"2023","journal-title":"J. Chem. Theory\nComput."},{"issue":"12","key":"2026101310104024000_cit6","doi-asserted-by":"publisher","first-page":"2848","DOI":"10.3390\/molecules25122848","article-title":"Understanding Surface Interaction\nand Inclusion Complexes\nbetween Piroxicam and Native or Crosslinked \u03b2-Cyclodextrins:\nThe Role of Drug Concentration","volume":"25","author":"Raffaini","year":"2020","journal-title":"Molecules 2020,\nVol. 25, Page 2848"},{"issue":"10","key":"2026101310104024000_cit7","doi-asserted-by":"publisher","first-page":"1047","DOI":"10.1517\/17460441.2015.1076389","article-title":"Simulation with Quantum Mechanics\/Molecular\nMechanics\nfor Drug Discovery","volume":"10","author":"Barbault","year":"2015","journal-title":"Expert Opin. Drug Discovery"},{"issue":"4","key":"2026101310104024000_cit8","doi-asserted-by":"publisher","first-page":"420","DOI":"10.3390\/coatings11040420","article-title":"Surface Chemistry,\nCrystal Structure, Size and Topography Role in the Albumin Adsorption\nProcess on TiO2 Anatase Crystallographic Faces and Its\n3D-Nanocrystal: A Molecular Dynamics Study","volume":"11","author":"Raffaini","year":"2021","journal-title":"Coatings"},{"issue":"5\u20136","key":"2026101310104024000_cit9","doi-asserted-by":"publisher","first-page":"817","DOI":"10.1016\/j.ccr.2008.04.007","article-title":"Are Classical\nMolecular Mechanics Calculations Still Useful in Bioinorganic Simulations?","volume":"253","author":"Zimmer","year":"2009","journal-title":"Coord. Chem. Rev."},{"issue":"4","key":"2026101310104024000_cit10","doi-asserted-by":"publisher","first-page":"1382","DOI":"10.1002\/jbm.a.32483","article-title":"Surface Hydration\nof Polymeric (Bio)Materials: A Molecular\nDynamics Simulation Study","volume":"92A","author":"Raffaini","year":"2010","journal-title":"J. Biomed. Mater.\nRes., Part A"},{"issue":"2","key":"2026101310104024000_cit11","doi-asserted-by":"publisher","first-page":"54","DOI":"10.1007\/s11249-021-01427-9","article-title":"Mechanical\nand Tribological Properties of Nitrile Rubber Reinforced by Nano-SiO2: Molecular Dynamics Simulation","volume":"69","author":"Liu","year":"2021","journal-title":"Tribol.\nLett."},{"issue":"11","key":"2026101310104024000_cit12","doi-asserted-by":"publisher","first-page":"4871","DOI":"10.1063\/1.472323","article-title":"Molecular Dynamics Simulations of a Fully Hydrated\nDipalmitoylphosphatidylcholine Bilayer with Different Macroscopic\nBoundary Conditions and Parameters","volume":"105","author":"Tieleman","year":"1996","journal-title":"J. Chem.\nPhys."},{"issue":"40","key":"2026101310104024000_cit13","doi-asserted-by":"publisher","first-page":"15873","DOI":"10.1021\/jp0477147","article-title":"System-Size Dependence of Diffusion Coefficients and\nViscosities from Molecular Dynamics Simulations with Periodic Boundary\nConditions","volume":"108","author":"Yeh","year":"2004","journal-title":"J. Phys. Chem. B"},{"issue":"11","key":"2026101310104024000_cit14","doi-asserted-by":"publisher","first-page":"5888","DOI":"10.3390\/ijms25115888","article-title":"Different\nDrug Mobilities in Hydrophobic Cavities of Host-Guest Complexes between\n\u03b2-Cyclodextrin and 5-Fluorouracil at Different Stoichiometries:\nA Molecular Dynamics Study in Water","volume":"25","author":"Raffaini","year":"2024","journal-title":"Int. J.\nMol. Sci."},{"key":"2026101310104024000_cit15","doi-asserted-by":"publisher","first-page":"6049","DOI":"10.1021\/j100378a077","article-title":"Molecular Dynamics Simulation of Single Ions in Aqueous\nSolutions: Effects of the Flexibility of the Water Molecules","volume":"94","author":"Guardia","year":"1990","journal-title":"J. Phys. Chem."},{"issue":"23","key":"2026101310104024000_cit16","doi-asserted-by":"publisher","first-page":"7830","DOI":"10.1021\/jp101759q","article-title":"Update of the CHARMM All-Atom Additive Force Field\nfor Lipids: Validation on Six Lipid Types","volume":"114","author":"Klauda","year":"2010","journal-title":"J.\nPhys. Chem. 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Macromol."},{"key":"2026101310104024000_cit19","doi-asserted-by":"publisher","first-page":"10150","DOI":"10.3390\/molecules190710150","article-title":"Challenges, Applications,\nand Recent Advances of Protein-Ligand Docking in Structure-Based Drug\nDesign","volume-title":"Molecules","author":"Grinter","year":"2014"},{"key":"2026101310104024000_cit20","doi-asserted-by":"publisher","first-page":"19","DOI":"10.1016\/j.softx.2015.06.001","article-title":"GROMACS: High\nPerformance\nMolecular Simulations through Multi-Level Parallelism from Laptops\nto Supercomputers","volume":"1\u20132","author":"Abraham","year":"2015","journal-title":"SoftwareX"},{"issue":"1","key":"2026101310104024000_cit21","doi-asserted-by":"publisher","first-page":"5068","DOI":"10.33011\/livecoms.1.1.5068","article-title":"From Proteins\nto Perturbed Hamiltonians: A Suite of Tutorials for the GROMACS-2018\nMolecular Simulation Package [Article v1.0]","volume":"1","author":"Lemkul","year":"2019","journal-title":"Living J. Comput. Mol. Sci."},{"key":"2026101310104024000_cit22","unstructured":"van der Spoel, D.; Caleman, C.; van Maaren, P.; Ghahremanpour, M. M.\n          Virtual\nChemistry. Available via the Internet at: https:\/\/virtualchemistry.org (accessed Jan. 26, 2026)."},{"issue":"8","key":"2026101310104024000_cit23","doi-asserted-by":"publisher","first-page":"4946","DOI":"10.1021\/acs.jctc.1c00195","article-title":"Q-Force:\nQuantum Mechanically Augmented Molecular Force Fields","volume":"17","author":"Sami","year":"2021","journal-title":"J. Chem. Theory Comput."},{"issue":"16","key":"2026101310104024000_cit24","doi-asserted-by":"publisher","first-page":"1701","DOI":"10.1002\/jcc.20291","article-title":"GROMACS: Fast, Flexible, and Free","volume":"26","author":"Van Der Spoel","year":"2005","journal-title":"J. Comput. Chem."},{"key":"2026101310104024000_cit25","unstructured":"Frisch, M. J.; Trucks, G. W.; Schlegel, H. B.; Scuseria, G. E.; Robb, M. A.; Cheeseman, J. 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J.\n          Gaussian 09;\n          Gaussian.Com, 2016, https:\/\/gaussian.com\/g09citation\/."},{"key":"2026101310104024000_cit26","doi-asserted-by":"publisher","first-page":"33","DOI":"10.1016\/0263-7855(96)00018-5","article-title":"VMD - Visual Molecular Dynamics","volume":"14","author":"Humphrey","year":"1996","journal-title":"J. Mol. Graph."},{"issue":"32","key":"2026101310104024000_cit27","doi-asserted-by":"publisher","first-page":"2740","DOI":"10.1002\/jcc.26426","article-title":"The Effect of Different Cutoff Schemes\nin Molecular\nSimulations of Proteins","volume":"41","author":"Diem","year":"2020","journal-title":"J. Comput. Chem."},{"issue":"1","key":"2026101310104024000_cit28","doi-asserted-by":"publisher","first-page":"637","DOI":"10.1063\/1.442716","article-title":"A Computer Simulation\nMethod for the Calculation of Equilibrium Constants for the Formation\nof Physical Clusters of Molecules: Application to Small Water Clusters","volume":"76","author":"Swope","year":"1982","journal-title":"J. Chem. Phys."},{"issue":"10","key":"2026101310104024000_cit29","doi-asserted-by":"publisher","first-page":"3637","DOI":"10.1021\/ct3000876","article-title":"Efficient\nAlgorithms for Langevin and DPD Dynamics","volume":"8","author":"Goga","year":"2012","journal-title":"J.\nChem. Theory Comput."},{"key":"2026101310104024000_cit30","doi-asserted-by":"publisher","first-page":"101084","DOI":"10.1016\/j.pecs.2023.101084","article-title":"Classical and Reactive Molecular\nDynamics: Principles\nand Applications in Combustion and Energy Systems","volume":"97","author":"Mao","year":"2023","journal-title":"Prog. Energy Combust. Sci."},{"key":"2026101310104024000_cit31","doi-asserted-by":"publisher","first-page":"263","DOI":"10.1016\/0010-4655(86)90113-X","article-title":"CHOICE OF\nTIMESTEP IN MOLECULAR DYNAMICS SIMULATION","volume":"40","author":"Fincham","year":"1986","journal-title":"Comput.\nPhys. Commun."},{"issue":"3","key":"2026101310104024000_cit32","doi-asserted-by":"publisher","first-page":"295","DOI":"10.1002\/jcc.540140306","article-title":"Conformational and Energetic Effects of Truncating\nNonbonded Interactions in an Aqueous Protein Dynamics Simulation","volume":"14","author":"Guenot","year":"1993","journal-title":"J. Comput. Chem."},{"issue":"12","key":"2026101310104024000_cit33","doi-asserted-by":"publisher","first-page":"10089","DOI":"10.1063\/1.464397","article-title":"Particle Mesh\nEwald: An N\u00b7log(N)\nMethod for Ewald Sums in Large Systems","volume":"98","author":"Darden","year":"1993","journal-title":"J. Chem.\nPhys."},{"key":"2026101310104024000_cit34","doi-asserted-by":"publisher","DOI":"10.1201\/9780367806934","article-title":"Computer Simulation Using Particles","author":"Hockney","year":"2021","journal-title":"Computer Simulation Using Particles"},{"issue":"1","key":"2026101310104024000_cit35","doi-asserted-by":"publisher","DOI":"10.1107\/s0907444902003451","article-title":"The Protein\nData Bank","volume":"28","author":"Berman","year":"2000","journal-title":"Nucleic Acids Res."},{"issue":"1","key":"2026101310104024000_cit36","doi-asserted-by":"publisher","first-page":"D437","DOI":"10.1093\/nar\/gkaa1038","article-title":"RCSB Protein\nData Bank: Powerful New Tools for Exploring 3D Structures of Biological\nMacromolecules for Basic and Applied Research and Education in Fundamental\nBiology, Biomedicine, Biotechnology, Bioengineering and Energy Sciences","volume":"49","author":"Burley","year":"2021","journal-title":"Nucleic Acids Res."},{"key":"2026101310104024000_cit37","unstructured":"Avogadro - Free cross-platform molecular\neditor - Avogadro. 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Soc."},{"issue":"2","key":"2026101310104024000_cit40","doi-asserted-by":"publisher","first-page":"459","DOI":"10.1021\/ct900549r","article-title":"Implementation\nof the Charmm Force Field in GROMACS: Analysis of Protein Stability\nEffects from Correction Maps, Virtual Interaction Sites, and Water\nModels","volume":"6","author":"Lindahl","year":"2010","journal-title":"J. Chem. Theory Comput."},{"key":"2026101310104024000_cit41","unstructured":"Berman, H. M.; Westbrook, J.; Feng, Z.; Gilliland, G.; Bhat, T. N.; Weissig, H.; Shindyalov, I. N.; Bourne, P. E.\n          The Protein\nData Bank; 2000; Vol. 28. Available via the\nInternet at: http:\/\/www.rcsb.org\/pdb\/status.html."},{"issue":"7","key":"2026101310104024000_cit42","doi-asserted-by":"publisher","first-page":"3499","DOI":"10.1021\/acs.jctc.5b00356","article-title":"Improved Peptide and Protein Torsional\nEnergetics with the OPLS-AA Force Field","volume":"11","author":"Robertson","year":"2015","journal-title":"J.\nChem. 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Chem. Soc."},{"issue":"45","key":"2026101310104024000_cit46","doi-asserted-by":"publisher","first-page":"11683","DOI":"10.1021\/jp073974n","article-title":"An Evaluation\nof Harmonic Vibrational\nFrequency Scale Factors","volume":"111","author":"Merrick","year":"2007","journal-title":"J. Phys. Chem. A"},{"issue":"14","key":"2026101310104024000_cit47","doi-asserted-by":"publisher","first-page":"6670","DOI":"10.1039\/c0cp02984j","article-title":"A Thorough Benchmark\nof Density Functional Methods\nfor General Main Group Thermochemistry, Kinetics, and Noncovalent\nInteractions","volume":"13","author":"Goerigk","year":"2011","journal-title":"Phys. Chem. Chem. Phys."},{"key":"2026101310104024000_cit48","unstructured":"Sami, S.\n          \n          Q-Force documentation. Available via the Internet at: https:\/\/qforce.readthedocs.io\/en\/latest\/ (accessed Jan. 14, 2026)."},{"issue":"9","key":"2026101310104024000_cit49","doi-asserted-by":"publisher","first-page":"4983","DOI":"10.1021\/acs.chemrev.5b00505","article-title":"An Empirical\nPolarizable Force Field Based on the Classical Drude Oscillator Model:\nDevelopment History and Recent Applications","volume":"116","author":"Lemkul","year":"2016","journal-title":"Chem. Rev."},{"issue":"46","key":"2026101310104024000_cit50","doi-asserted-by":"publisher","first-page":"13473","DOI":"10.1021\/jp206665w","article-title":"Hydrogen Bonding\nand\nMolecular Aggregates in Liquid Methanol, Ethanol, and 1-Propanol","volume":"115","author":"Vrhovs\u030cek","year":"2011","journal-title":"J. Phys. Chem. B"},{"issue":"19","key":"2026101310104024000_cit51","doi-asserted-by":"publisher","first-page":"194501","DOI":"10.1063\/1.4829760","article-title":"Liquid\nChloroform Structure from\nComputer Simulation with a Full Ab Initio Intermolecular Interaction\nPotential","volume":"139","author":"Yin","year":"2013","journal-title":"J. Chem. Phys."},{"key":"2026101310104024000_cit52","volume-title":"The Properties of Solvents","author":"Marcus","year":"1998"},{"issue":"1","key":"2026101310104024000_cit53","doi-asserted-by":"publisher","DOI":"10.1063\/1.2408420","article-title":"Canonical Sampling\nthrough Velocity Rescaling","volume":"126","author":"Bussi","year":"2007","journal-title":"J. Chem. Phys."},{"issue":"11","key":"2026101310104024000_cit54","doi-asserted-by":"publisher","DOI":"10.1063\/5.0020514","article-title":"Pressure Control Using Stochastic\nCell Rescaling","volume":"153","author":"Bernetti","year":"2020","journal-title":"J. Chem. 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