Implementing replica exchange molecular dynamics using work queue

Replica exchange molecular dynamics (REMD) has been used by researchers to improve sampling rates in molecular dynamics simulations. In traditional t-REMD, individual replicas run in parallel at different temperatures. The neighboring replicas exchange temperature based on a criterion after a time interval. In this research, we implemented REMD on a computational framework, Work Queue, and evaluated the performance of Work Queue based REMD. The master-worker architecture was used in our implementation. All replicas were assigned to workers, outputs from replicas on workers were gathered and sent to the master and processed on the master. NAMD was used to carry out individual molecular dynamics simulations. The programming language used in the implementation was C. We evaluated the performance of Work Queue based REMD. The experimental results demonstrate linear scalability for lower number of replicas.