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PACKMOL: A package for building initial configurations for molecular dynamics simulations by L. Martínez; R. Andrade; E. G. Birgin; J. M. Martínez is a Chemistry article available to read on EtoBox.

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## 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 mole

Who reads PACKMOL: A package for building initial configurations for molecular dynamics simulations?

Author

L. Martínez; R. Andrade; E. G. Birgin; J. M. Martínez

Publisher

Wiley

Published

2009

Language

EN

Field

Chemistry (Physical Sciences)