PeerMD, a P2P molecular dynamics simulation frame-work based on Web services is proposed. It utilizes rich free CPU time and network bandwidth of P2P networks to provide enough resources for dynamics simulation of bio-macromolecule, and has resolved the problem that it is difficult to interoperate between heterogeneous peers in P2P environment through Web services. Structure of PeerMD is given. Function, input and output of molecular dynamics simulation Web service are defined. Processes of publishing, discovering and invoking of molecular dynamics simulation Web service based on multi-level SuperPeer are given. A protocol system of PeerMD is implemented on a basic P2P platform JXTA, and experimental simulations of tumor necrosis fact alpha (TNF-α) and two mutations of it are executed on the protocol system. Simulation results show that PeerMD can speed up molecular dynamics simulation perfectly.
