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

2009/02/19 by L. Martínez, Leandro Martı́nez, Ricardo Andrade +5 · 104 citations
Biochemistry, Genetics and Molecular Biology · Chemistry · Physics and Astronomy · #Advanced NMR Techniques and Applications #Protein Structure and Dynamics #Spectroscopy and Quantum Chemical Studies

paper · pdf · doi:10.1002/jcc.21224

openalex publication_date 2009/02/19 · openalex created_date 2016/06/24 · openalex updated_date 2026/07/31

Abstract

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 a 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 straightforward. 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 can be built, as micelles, lipid double-layers, etc. The packing time for state-of-the-art molecular dynamics systems varies from 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 can be downloaded from http://www.ime.unicamp.br/~martinez/packmol/.

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