A test problem for molecular dynamics integrators
نویسندگان
چکیده
منابع مشابه
Time Integrators for Molecular Dynamics
This paper invites the reader to learn more about time integrators for Molecular Dynamics simulation through a simple MATLAB implementation. An overview of methods is provided from an algorithmic viewpoint that emphasizes long-time stability and finite-time dynamic accuracy. The given software simulates Langevin dynamics using an explicit, second-order (weakly) accurate integrator that exactly ...
متن کاملA common, avoidable source of error in molecular dynamics integrators.
In constrained molecular dynamics simulations using some of the most popular MD codes, calculation of the velocities of constrained particles is based solely on the differences in particle positions during two successive time steps. This creates a numerical instability that we show to be signicant in a typical single-precision floating-point simulation. We describe a simple modification that el...
متن کاملA Test Set for Molecular Dynamics Algorithms
This article describes a collection of model problems for aiding numerical analysts, code developers and others in the design of computational methods for molecular dynamics (MD) simulation. Common types of calculations and desirable features of algorithms are surveyed, and these are used to guide selection of representative models. By including essential features of certain classes of molecula...
متن کاملIntegrators for quantum dynamics: a numerical analyst’s brief review
This note, written for the NIC Winter School ”Quantum Simulations of Complex Many-Body Systems: From Theory to Algorithms”, discusses and compares – in theoretical respects – various old and new approaches to numerical time integration for quantum dynamics: implicit vs. exponential midpoint rule; splitting, Chebyshev and Lanczos approximations to the exponential; Magnus integrators; integrators...
متن کاملMolecular dynamics integration and molecular vibrational theory. I. New symplectic integrators.
New symplectic integrators have been developed by combining molecular dynamics integration with the standard theory of molecular vibrations to solve the Hamiltonian equations of motion. The presented integrators analytically resolve the internal high-frequency molecular vibrations by introducing a translating and rotating internal coordinate system of a molecule and calculating normal modes of ...
متن کاملذخیره در منابع من
با ذخیره ی این منبع در منابع من، دسترسی به آن را برای استفاده های بعدی آسان تر کنید
ژورنال
عنوان ژورنال: IMA Journal of Numerical Analysis
سال: 2005
ISSN: 0272-4979,1464-3642
DOI: 10.1093/imanum/drh023