Paper Citing NAMD - Abstract
Koishi, Takahiro; Takeichi, Hironori
An efficiently extendable and fine-grain parallelised molecular dynamics simulation program: Mid
MOLECULAR SIMULATION, 41:801-807, AUG 13 2015
A new implementation of molecular dynamics simulation is presented. We employed policy-based design to achieve static polymorphism within our simulation programs. This technique provides flexibility and extensibility without additional if-statement branching in the simulation program development. It is shown that policy-based implementation prevents computational performance degradation. We used a fine-grained domain decomposition scheme to parallelise the simulation program. The smaller size decomposition reduces the total amount of inter-processing-core communication and affords good scalability for parallel calculation of short-range forces. The calculation of long-range interactions limits the total scalability. For enhanced performance at high levels of parallelism, the calculation methods for long-range interactions should be improved.
