Journal ArticleDOI
On the orthogonal transformation used for structural comparisons
Reads0
Chats0
TLDR
In this article, a constrained least-squares procedure is used to find a rotation matrix that minimizes or maximizes the sum of the squared distances between corresponding atoms for two structures.Abstract:
Rotation matrices that minimize or maximize the sum of the squared distances between corresponding atoms for two structures are found using a constrained least-squares procedure solved analytically as an eigenvalue problem in quaternion parameters.read more
Citations
More filters
Journal ArticleDOI
OLEX2: a complete structure solution, refinement and analysis program
TL;DR: OLEX2 seamlessly links all aspects of the structure solution, refinement and publication process and presents them in a single workflow-driven package, with the ultimate goal of producing an application which will be useful to both chemists and crystallographers.
Journal ArticleDOI
PLUMED 2: New feathers for an old bird
TL;DR: This work presents PLUMED 2 here—a complete rewrite of the code in an object-oriented programming language (C++), which introduces greater flexibility and greater modularity, which both extends its core capabilities and makes it far easier to add new methods and CVs.
Journal ArticleDOI
PLUMED: a portable plugin for free-energy calculations with molecular dynamics
Massimiliano Bonomi,Davide Branduardi,Giovanni Bussi,Carlo Camilloni,Davide Provasi,Paolo Raiteri,Davide Donadio,Fabrizio Marinelli,Fabio Pietrucci,Ricardo A. Broglia,Ricardo A. Broglia,Michele Parrinello +11 more
TL;DR: A series of routines that can be interfaced with the most popular classical molecular dynamics codes through a simple patching procedure, which leaves the possibility for the user to exploit many different MD engines depending on the system simulated and on the computational resources available.
Journal ArticleDOI
Metadynamics: a method to simulate rare events and reconstruct the free energy in biophysics, chemistry and material science
TL;DR: Metadynamics is a powerful algorithm that can be used both for reconstructing the free energy and for accelerating rare events in systems described by complex Hamiltonians, at the classical or at the quantum level as discussed by the authors.
Journal ArticleDOI
Iterative model building, structure refinement and density modification with the PHENIX AutoBuild wizard
Thomas C. Terwilliger,Ralf W. Grosse-Kunstleve,Pavel V. Afonine,Nigel W. Moriarty,Peter H. Zwart,Li-Wei Hung,Randy J. Read,Paul D. Adams +7 more
TL;DR: The PHENIX AutoBuild wizard as discussed by the authors is a highly automated tool for iterative model building, structure refinement and density modification using RESOLVE model building and statistical density modification.