Paper Citing NAMD - Abstract
Yoshii, Noriyuki; Andoh, Yoshimichi; Fujimoto, Kazushi; Kojima, Hidekazu; Yamada, Atsushi; Okazaki, Susumu
MODYLAS: A Highly Parallelized General-Purpose Molecular Dynamics Simulation Program
INTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY, 115:342-348, MAR 5 2015
A large number of molecular dynamics (MD) simulations have been carried out so far on personal computer clusters and conventional supercomputers using general-purpose MD software such as NAMD, GROMACS, CHARMM, and AMBER. The development of MD simulation program is closely related to the architecture of the computers. Recent trend of MD simulation is headed to large-scale calculation, long-time calculation of small systems, and calculation for large statistics. The most challenging one is the large-scale calculation. To realize the large-scale calculation, we have to efficiently control the massively parallel supercomputers with several 10 thousands of nodes. There, it is essential to develop software having a compatibility of such computer architecture. Recently, we have developed general-purpose MD software MODYLAS (MOlecular DYnamics simulation software for LArge Systems) for massively parallel supercomputers such as K-computer. Here, we describe the outline, important features, and computation of MODYLAS. An example result of the 200 ns-MD simulation of the viral capsid system consisting of about 6,500,000 atoms is also presented. (c) 2014 Wiley Periodicals, Inc.
