Paper Citing NAMD - Abstract
Sun, Lin; Le, Chinh; Saied, Faisal; Murthy, Jayathi Y.
Performance of a parallel molecular dynamics program for computation of thermal properties
NUMERICAL HEAT TRANSFER PART B-FUNDAMENTALS, 51:315-331, 2007
The parallel performance of classical molecular dynamics simulations of the thermal properties of solid-state materials is evaluated. Computations are validated by predicting the bulk silicon thermal conductivity as a function of temperature. The performance of the computational algorithm and software are tested on three different architectures, including the IBM BlueGene, the IBM Power 4+, and an Intel Xeon Linux cluster, corresponding to different combinations of processor speeds, communications bandwidth, and latency. Two popular three- body potentials used for silicon simulation are evaluated and compared. In addition, the popular Lennard-Jones potential is used to investigate to role of cutoff distance on parallel performance.
