José Mario Martínez

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

Adequate initial configurations for molecular dynamics simulations consist of arrangements of molecules distributed in space in such a way to approximately represent the systems 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/.

Nonmonotone Spectral Projected Gradient Methods on Convex Sets

Nonmonotone projected gradient techniques are considered for the minimization of differentiable functions on closed convex sets. The classical projected gradient schemes are extended to include a nonmonotone steplength strategy that is based on the Grippo--Lampariello--Lucidi nonmonotone line search. In particular, the nonmonotone strategy is combined with the spectral gradient choice of steplength to accelerate the convergence process. In addition to the classical projected gradient nonlinear path, the feasible spectral projected gradient is used as a search direction to avoid additional trial projections during the one-dimensional search process. Convergence properties and extensive numerical results are presented.

Packing optimization for automated generation of complex system's initial configurations for molecular dynamics and docking

Molecular Dynamics is a powerful methodology for the comprehension at molecular level of many chemical and biochemical systems. The theories and techniques developed for structural and thermodynamic analyses are well established, and many software packages are available. However, designing starting configurations for dynamics can be cumbersome. Easily generated regular lattices can be used when simple liquids or mixtures are studied. However, for complex mixtures, polymer solutions or solid adsorbed liquids (for example) this approach is inefficient, and it turns out to be very hard to obtain an adequate coordinate file. In this article, the problem of obtaining an adequate initial configuration is treated as a “packing” problem and solved by an optimization procedure. The initial configuration is chosen in such a way that the minimum distance between atoms of different molecules is greater than a fixed tolerance. The optimization uses a well‐known algorithm for box‐constrained minimization. Applications are given for biomolecule solvation, many‐component mixtures, and interfaces. This approach can reduce the work of designing starting configurations from days or weeks to few minutes or hours, in an automated fashion. Packing optimization is also shown to be a powerful methodology for space search in docking of small ligands to proteins. This is demonstrated by docking of the thyroid hormone to its nuclear receptor.

On Augmented Lagrangian Methods with General Lower-Level Constraints

Augmented Lagrangian methods with general lower-level constraints are considered in the present research. These methods are useful when efficient algorithms exist for solving subproblems in which the constraints are only of the lower-level type. Inexact resolution of the lower-level constrained subproblems is considered. Global convergence is proved using the constant positive linear dependence constraint qualification. Conditions for boundedness of the penalty parameters are discussed. The resolution of location problems in which many constraints of the lower-level set are nonlinear is addressed, employing the spectral projected gradient method for solving the subproblems. Problems of this type with more than

Algorithm 813: SPG—Software for Convex-Constrained Optimization

3 \times 10^6

Large-Scale Active-Set Box-Constrained Optimization Method with Spectral Projected Gradients

variables and

Spectral residual method without gradient information for solving large-scale nonlinear systems of equations

14 \times 10^6

Practical quasi-Newton methods for solving nonlinear systems

constraints are solved in this way, using moderate computer time. All the codes are available at http://www.ime.usp.br/

Augmented Lagrangian methods under the constant positive linear dependence constraint qualification

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A new trust region algorithm for bound constrained minimization

egbirgin/tango/.