Demonstration Materials for Educators
While the algorithms powering Amber are published in numerous journals, and
practical instructions for using Amber are provided on
this website, neither of these sets of
materials offers a hands-on explanation of how the code actually works.
The purpose of this new section of the website is to walk through the relevant
algorithms with stand-alone, richly commented codes and examples. We hope that
this will prompt more interest in Amber itself and in computational chemistry
generally. These materials are by no means a complete exposition of everything
that Amber does, but we anticipate adding more as time permits.
Article 1: Smooth Particle-Mesh
Ewald for Collections of Ions
This demonstration shows how the well-known Smooth Particle-Mesh Ewald
method (a special case of the Particle-Particle / Particle-Mesh or
P3M algorithm) handles infinite electrostatics in simulations
invoking periodic boundary conditions.
By David Cerutti
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