Paper Citing NAMD - Abstract
Palmer, Bruce; Kathmann, Shawn; Krishnan, Manojkumar; Tipparaju, Vinod; Nieplocha, Jarek
The use of processor groups in molecular dynamics simulations to sample free-energy states
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 3:583-592, MAR-APR 2007
Molecular dynamics calculations composed of many independent simulations are frequently encountered in free-energy calculations, as well as many other simulation approaches. In principle, the availability of a large number of independent tasks should make possible the development of highly scalable parallel code that executes these tasks concurrently. This paper discusses the use of processor groups to write simulation codes of this type and describes results for a code that evaluates the volume dependence of the Helmholtz free energy for clusters of an immiscible fluid in a solvent. The results show that very high levels of scalability can be achieved using processor groups with corresponding reductions in the time to completion. The main limitation to scaling appears to be a load imbalance due to variations in the execution times of the individual tasks.
