Large Scale Molecular Dynamics Simulation Using MD-Engine

Abstract

Recently, demands for computing and designing large complex systems, such as proteins, biomembrain and so on, grow tremendously. For those systems, accurate calculation of non-bonding interactions becomes crucial to predict correct stable structures and thermodynamic properties in molecular dynamics(MD) simulations. However, for examples, truncation of Coulombic interaction must be taken very large and consequently calculation cost scales as O(N²⁾ Special purpose molecular dynamics(MD) hardware accelerator, which is called the MD-Engine, has been used to overcome this difficulty and applied to several complex systems. The MD-Engine consists of custum prosessors that calculate pairwise potentials and forces in parallel. A user just has to send coordinate of atoms and force field parameters, then receive forces and potential energy. Our test calculations show good linear scaling with the system size.