PACKMOL: a package for building initial configurations for molecular dynamics simulations.
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TLDR
This work has developed a code able to pack millions of atoms, grouped in arbitrarily complex molecules, inside a variety of three‐dimensional regions, which can be intersections of spheres, ellipses, cylinders, planes, or boxes.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/.read more
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Journal ArticleDOI
Avogadro: an advanced semantic chemical editor, visualization, and analysis platform
Marcus D. Hanwell,Marcus D. Hanwell,Donald Ephraim Curtis,David Lonie,Tim Vandermeersch,Eva Zurek,Geoffrey R. Hutchison +6 more
TL;DR: The work presented here details the Avogadro library, which is a framework providing a code library and application programming interface (API) with three-dimensional visualization capabilities; and has direct applications to research and education in the fields of chemistry, physics, materials science, and biology.
Journal ArticleDOI
CHARMM-GUI Membrane Builder Toward Realistic Biological Membrane Simulations
Emilia L. Wu,Xi Cheng,Sunhwan Jo,Huan Rui,Kevin C. Song,Eder M. Dávila-Contreras,Yifei Qi,Jumin Lee,Viviana Monje-Galvan,Richard M. Venable,Jeffery B. Klauda,Wonpil Im +11 more
TL;DR: The new features and major improvements in Membrane Builder that allow users to robustly build realistic biological membrane systems are described, including addition of new lipid types, including phosphoinositides, cardiolipin (CL), sphingolipids, bacterial lipids, and ergosterol.
Journal ArticleDOI
Tinker 8: Software Tools for Molecular Design.
Joshua A. Rackers,Zhi Wang,Chao Lu,Marie L. Laury,Louis Lagardère,Michael J. Schnieders,Jean-Philip Piquemal,Pengyu Ren,Jay W. Ponder +8 more
TL;DR: The Tinker software, currently released as version 8, is a modular molecular mechanics and dynamics package written primarily in a standard, easily portable dialect of Fortran 95 with OpenMP extensions, which supports a wide variety of force fields.
Journal ArticleDOI
Computational Lipidomics with insane: A Versatile Tool for Generating Custom Membranes for Molecular Simulations
Tsjerk A. Wassenaar,Tsjerk A. Wassenaar,Helgi I. Ingólfsson,Rainer A. Böckmann,D. Peter Tieleman,Siewert J. Marrink +5 more
TL;DR: A comprehensive method for building membrane containing systems, characterized by simplicity and versatility, and a survey of properties for a large range of lipids as a start of a computational lipidomics project.
Journal ArticleDOI
A rechargeable zinc-air battery based on zinc peroxide chemistry
Wei Sun,Fei Wang,Bao Zhang,Mengyi Zhang,Verena Küpers,Xiao Ji,Claudia Theile,Peter Bieker,Kang Xu,Chunsheng Wang,Martin Winter,Martin Winter +11 more
TL;DR: In this paper, a zinc-O2/zinc peroxide (ZnO2) chemistry was proposed, which enables highly reversible redox reactions in zinc-air batteries.
References
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Book
Numerical Methods for Unconstrained Optimization and Nonlinear Equations (Classics in Applied Mathematics, 16)
TL;DR: In this paper, Schnabel proposed a modular system of algorithms for unconstrained minimization and nonlinear equations, based on Newton's method for solving one equation in one unknown convergence of sequences of real numbers.
Book
Numerical methods for unconstrained optimization and nonlinear equations
TL;DR: Newton's Method for Nonlinear Equations and Unconstrained Minimization and methods for solving nonlinear least-squares problems with Special Structure.
Journal ArticleDOI
A fast algorithm for particle simulations
TL;DR: An algorithm is presented for the rapid evaluation of the potential and force fields in systems involving large numbers of particles whose interactions are Coulombic or gravitational in nature, making it considerably more practical for large-scale problems encountered in plasma physics, fluid dynamics, molecular dynamics, and celestial mechanics.
Book
Linear and nonlinear programming
David G. Luenberger,Yinyu Ye +1 more
TL;DR: Strodiot and Zentralblatt as discussed by the authors introduced the concept of unconstrained optimization, which is a generalization of linear programming, and showed that it is possible to obtain convergence properties for both standard and accelerated steepest descent methods.
Journal ArticleDOI
Automated builder and database of protein/membrane complexes for molecular dynamics simulations.
Sunhwan Jo,Taehoon Kim,Wonpil Im +2 more
TL;DR: The efficacy of Membrane Builder is illustrated by its applications to 12 transmembrane and 3 interfacial membrane proteins, whose fully equilibrated systems with three different types of lipid molecules and two types of system shapes are freely available on the CHARMM-GUI website.