REMD toolkit: A Composable Software to Generate Parallelized Simulation Programs
M. Ito and U. Nagashima
Keywords: replica-exchange, molecular dynamics, object-oriented framework, parallel
We developed a toolkit to generate a replica exchange method program which is suitable to solve the multiple-minima problem that prevents the accurate estimation of thermodynamical quantities. The toolkit was designed as a set of software components, so that any new variant of simulation program can be built by assembling suitable components. They are categorized according to three types of functions: parallelization of simulation programs, selection of sampling algorithms, and incorporation of an arbitrary force field implementation into the program. The extensibility and efficiency of the toolkit was demonstrated by generating a new variant of replica exchange method program which implements CHARMM force field. It was shown that the replica exchange scheme not only reduces the total computational cost with the increase in the number of replicas but achieves almost linear--speedup with the number of CPUs.
Nanotech 2004 Conference Technical Program Abstract