Implementing Replica Exchange Molecular Dynamics Using Work Queue
Replica exchange molecular dynamics (REMD) has been used by researchers for improving sampling rate. In traditional t-REMD, individual replicas run in parallel at different temperatures. Temperatures of the neighboring replicas are exchanged based on a criterion. In this research, we will implement REMD on Work Queue framework and evaluate the performance of the Work Queue based REMD and compare its performance against that in parallel environment. The master-worker framework will be applied into the implementation. All replicas will be assigned to workers; outputs from all replicas will be gathered in master and finish processing. NAMD will be the MD software package to use in the implementation for the MD simulation. Programming language used in this project will be C.