PACKMOL: A package for building initial configurations for molecular dynamics simulations

By Leandro Martínez, R. Andrade, Ernesto G. Birgin, José Mario Martínez. Journal of Computational Chemistry, 2009

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CHARMM-GUI Membrane Builder for Complex Biological Membrane Simulations with Glycolipids and Lipoglycans. (2018, methodology): “As all the aforementioned tools are for modeling single glycan/glycolipid/lipoglycan structures, building a simulation system with the generated glycolipid/lipolgycan structures requires additional molecular packing tools, such as PACKMOL 24 or MembraneEditor 25 .”
Buried interface molecular hybrid for inverted perovskite solar cells (2024, positive): “The SAMs layer in four heterojunction models contains the following: (1) 90 Me-4PACz molecules; (2) 90 Me-4PACz and 30 BA molecules; (3) 90 Me-4PACz and 30 NA molecules; and (4) 90 Me-4PACz and 30 TA molecules, which were randomly generated between the surfaces by the Packmol program 38 .”
Avogadro: an advanced semantic chemical editor, visualization, and analysis platform (2012, background): “Packmol is a third-party package designed to create initial “packed” conﬁgurations of molecules for molecular dynamics or other simulations [75,76].”
Development and Benchmarking of Open Force Field 2.0.0: The Sage Small Molecule Force Field (2023, neutral): “For the full reﬁt of the Sage force ﬁeld, a total of 30 LJ parameters ( 𝑅 𝑚𝑖𝑛 ∕2 ,𝜖 for 15 LJ types) representing carbon, hydrogen, oxygen, nitrogen, chlorine and bromine environments were included.”