Examining the feasibility of reconfigurable models for molecular dynamics simulation

Abstract

A Molecular Dynamics (MD) system is defined by the position and momentum of particles and their interactions. The dynamics of a system can be evaluated by an N-body problem and the simulation is continued until the energy reaches equilibrium. Many applications use MD for biomolecular simulations and the simulations are performed in multiscale of time and length. The simulations of the relevant scales require strong and fast computing power, but it is even beyond the reach of current fastest supercomputers. In this paper, we design R-Mesh Algorithms that require O(N) time complexity for the Direct method for MD simulations and O(r)+O(logM) time complexity for the Multigrid method, where r is N/M and M is the size of R-Mesh. Our work supports the theory that reconfigurable models are a good direction for biological studies which require high computing power. © 2008 Springer-Verlag Berlin Heidelberg.