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

Abstract

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

A molecular dynamics investigation into the adsorption behavior inside {001} kaolinite and {1014} calcite nano-scale channels: the case with confined hydrocarbon liquid, acid gases, and water

“…Orthorhombic simulation cells were considered with Periodic Boundary Condition (PBC) in x-y directions. The Packmol package (Martínez et al 2009) was used to construct the initial configuration of molecules in the simulation cell.…”

Viscosities of the Mixtures of 1-Ethyl-3-Methylimidazolium Chloride with Water, Acetonitrile and Glucose: A Molecular Dynamics Simulation and Experimental Study

“…A particle-particle particle mesh solver with a precision of 10 -4 was employed to treat long-range electrostatic interactions. PACKMOL 44 was used to generate the initial state of the system in a large cubic box, followed by * To whom correspondence should be addressed. E-mail: (B.S.)…”

On the Denaturation Mechanisms of the Ligand Binding Domain of Thyroid Hormone Receptors

“…The structures of TRR and TR bound to Triac were recently obtained by our research group and were refined to 2.0 and 2.5 Å, respectively. 26 The complete simulated systems were built with Packmol, 40,41 containing the LBD of either subtype, water, and one counterion for each charged residue for electroneutrality: 43 Na + and 30 Cl -ions for TRR and 43 Na + and 30 Cl -for TR bound to Triac. For the apo-structures of both LBD subtypes there is one less Na + in solution.…”