Performance and cost effectiveness of a cluster of workstations and MD-GRAPE 2 for MD simulations
J.V. Sumanth, David R. Swanson, Hong Jiang · 2004
Molecular dynamics (MD) simulations are performed on systems of various sizes up to 32 million atoms. Performance is compared between an MD-GRAPE 2 board, specialized hardware optimized for MD, and a general purpose cluster computer utilizing varied numbers of processors for both short- and long-range potentials. While it is possible to outperform a single MD-GRAPE 2 board with a sufficient number of processors, tests verses a local cluster and comparison of original purchase price show the MD-GRAPE 2 board is often cost-effective. Potential-specific considerations are discussed.