PACKMOL: A Package for Building Initial Configurations for Molecular Dynamics Simulations

Autor(es)

Martinez, L. ^[1] ; Andrade, R. ^[2] ; Birgin, E. G. ^[2] ; Martinez, J. M. ^[3]

Afiliação do(s) autor(es)

^[1] Univ Estadual Campinas, IQ UNICAMP, Dept Chem Phys, Campinas, SP - Brazil

^[2] Univ Sao Paulo, IME USP, Dept Comp Sci, BR-05508090 Sao Paulo - Brazil

^[3] Univ Estadual Campinas, IMECC UNICAMP, Dept Appl Math, BR-13081970 Campinas, SP - Brazil

• Tipo de documento: Artigo Científico
• Fonte: Journal of Computational Chemistry; v. 30, n. 13, p. 2157-2164, OCT 2009.
• Citações Web of Science: 1778

Resumo

Adequate initial configurations for molecular dynamics simulations consist of arrangements of molecules distributed in space in such a way to approximately represent the system's overall structure. In order that the simulations are not disrupted by large van der Waals repulsive interactions, atoms from different molecules Must keep safe pairwise distances. Obtaining Such a molecular arrangement can be considered it packing problem: Each type molecule must satisfy spatial constraints related to the geometry of the system, and the distance between atoms of different molecules Must be greater than some specified tolerance. We have developed a code able to pack millions of atoms. grouped in arbitrarily complex molecules, inside a variety of three-dimensional regions. The regions may be intersections of spheres, ellipses, cylinders, planes, or boxes. The user must provide only the structure of one molecule of each type and the geometrical constraints that each type of molecule must satisfy. Building complex mixtures, interfaces, solvating biomolecules in water, other solvents, or mixtures of solvents, is straight forward. In addition. different atoms belonging to the same molecule may also be restricted to different spatial regions, in Such a way that more ordered molecular arrangements call be built, as micelles. lipid double-layers, etc. The packing time for state-of-the-art molecular dynamics systems varies front a few seconds to a few Minutes in a personal Computer. The input files are simple and Currently compatible with PDB, Tinker, Molden, or Moldy coordinate files. The package is distributed as free software and call be downloaded front http://www.ime.unicamp.br/similar to martinez/packmol/. (C) 2009 Wiley Periodicals. Inc. J Comput Chem 30: 2157-2164, 2009 (AU)