Paper Citing NAMD - Abstract
Bannerman, M. N.; Sargant, R.; Lue, L.
DynamO: A Free O(N) General Event-Driven Molecular Dynamics Simulator
JOURNAL OF COMPUTATIONAL CHEMISTRY, 32:3329-3338, NOV 30 2011
Molecular dynamics algorithms for systems of particles interacting through discrete or "hard" potentials are fundamentally different to the methods for continuous or "soft" potential systems. Although many software packages have been developed for continuous potential systems, software for discrete potential systems based on event-driven algorithms are relatively scarce and specialized. We present DynamO, a general event-driven simulation package, which displays the optimal O(N) asymptotic scaling of the computational cost with the number of particles N, rather than the O(N log N) scaling found in most standard algorithms. DynamO provides reference implementations of the best available event-driven algorithms. These techniques allow the rapid simulation of both complex and large (>10(6) particles) systems for long times. The performance of the program is bench-marked for elastic hard sphere systems, homogeneous cooling and sheared inelastic hard spheres, and equilibrium Lennard-Jones fluids. This software and its documentation are distributed under the GNU General Public license and can be freely down-loaded from http://marcusbannerman.co.uk/dynamo. (C) 2011 Wiley Periodicals, Inc. J Comput Chem 32: 3329-3338, 2011
