Paper Citing NAMD - Abstract
Lupo, J.A.; Wang, Z.Q.; McKenney, A.M.; Pachter, R.; Mattson, W.
A large scale molecular dynamics simulation code using the fast multipole algorithm (FMD): performance and application
JOURNAL OF MOLECULAR GRAPHICS & MODELLING, 21:89-99, OCT 2002
We present the performance of the fast classical molecular dynamics (MD) code, fast molecular dynamics (FMD), designed for efficient, object-oriented, and scalable large scale simulations, and summarize its application to a liquid crystalline cluster. FMD uses an implementation of the three-dimensional fast multipole method, developed in our group. The fast multipole method offers an efficient way (order O(N)) to handle long range electrostatic interactions, thus, enabling more realistic simulations of large molecular systems. Performance testing was carried out on IBM SP2, SGI Origin 2000, and CRAY T3E massively parallel systems using the MPI massage passing library. The electrostatic forces were tested on models of up to 100,000 randomly placed charges, and on protein and liquid crystalline molecular systems of over 99,000 atoms. Tests on the stability of the method are presented, along with comparisons with direct calculations, the (NAMD)2 code, and the physical multipole-based cell-multipole method. (C) 2002 Published by Elsevier Science Inc.
