Paper Citing NAMD - Abstract
Mederski, Jaroslaw; Mikulski, Lukasz; Bala, Piotr
Asynchronous parallel molecular dynamics simulations
PARALLEL PROCESSING AND APPLIED MATHEMATICS, 4967:439-446, 2008
Dynamic development of parallel computers makes them standard tool for large simulations. The technology achievements are not followed by the progress in scalable code design. The molecular dynamics is a good example. In this paper we present novel approach to the molecular dynamics which is based on the new asynchronous parallel algorithm inspired by the novel computer architectures. We present also implementation of the algorithm written in Java. Presented code is object-oriented, multithread and distributed. The performance data is also available.
