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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See also:
ComplexMixtures.jl MDLovoFit
CellListMap.jl LovoAlign
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Packmol citation

Please cite the following reference if the Packmol package was useful:

L. Martínez, R. Andrade, E. G. Birgin, J. M. Martínez. Packmol: A package for building initial configurations for molecular dynamics simulations. Journal of Computational Chemistry, 30(13):2157-2164, 2009.

Download paper: (pdf file, 232 kb)

And please also cite the following article if mentioning the packing strategy of Packmol:

J. M. Martínez and L. Martínez. Packing optimization for automated generation of complex system's initial configurations for molecular dynamics and docking. Journal of Computational Chemistry, 24(7):819-825, 2003.

Download Technical Report: (pdf file, 270 kb) or (ps file, 623 kb)

Further information about the research projects being developed by our groups can be found at our research pages:

Leandro Martínez -
Institute of Chemistry, State University of Campinas

José Mario Martínez -
Institute of Mathematics, Statistics and Scientific Computation - University of Campinas

Ernesto G. Birgin -
Institute of Mathematics and Statistics - University of São Paulo