Initial configurations for Molecular Dynamics Simulations by packing optimization

Institute of Chemistry and Institute of Mathematics
University of Campinas
Institute of Mathematics and Statistics
University of São Paulo
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Practical applications

These examples are from simulations that have been performed by Packmol users. We encourage users to report examples for this page. Send an one-line description of your system, a picture, your name, and work references to and your example will be included in this list.

Poly(ethylene oxide) doped with LiTFSI in contact with a Li metal surface.

See: M. Ebadi, L. T. Costa, C. M. Araujo, D. Brandell, Eletrochim. Acta 234, 43-51, 2017. [LINK]
Lipase solvated by water and carbon dioxide.

See: R. L. Silveira, J. Martínez, M. S. Skaf, L. Martínez, "Enzyme Microheterogeneous Hydration and Stabilization in Supercritical Carbon Dioxide" J. Phys. Chem. B 116, 5651-5678, 2012. [PDF]
DMSO solutions for studying cryoprotection.
Courtesy of Jestin Mandumpal.

See: J. B. Mandunpal, C. Kreck, R. L. Mancera, "A molecular mechanism of solvent cryoprotection in aqueous DMSO solutions". Phys. Chem. Chem. Phys. 13, 3839-3842 (2011).
Polyoxyethylene with ions.
Courtesy of Luciano T. Costa

See: L. T. Costa, M. C. C. Ribeiro, "Molecular dynamics simulation of polymer electrolytes based on poly(ethylene oxide) and ionic liquids. I. Structural properties", J. Chem. Phys. 124, 184902 (2006).
Coumarin in an interface of water and zirconia.
Courtesy of L. R. Martins.

See: L. R. Martins, M. S. Skaf and B. M. Ladanyi, "Solvation Dynamics at the Water/Zirconia Interface: Molecular Dynamics Simulations", J. Phys. Chem. B 108 (51) 19687-19697, 2004.
Interface of water and chloroform.
Courtesy of N. H. Moreira.

See: N. H. Moreira and M. S. Skaf, "Structural characterization of the H2O/CCl4 liquid interface using molecular dynamics simulations", Prog. Coll. Pol. Sci. 128, p. 81, 2004.
Coumarin, water and sodium ions encapsulated in a zeolite.
Courtesy of L. R. Martins.
DNA double strand solvated by water and sodium ions.
Courtesy of M. T. Sonoda.
Supercritical carbon dioxide solvating caffeine.
Courtesy of F. W. Favero.