PeerMD: A P2P Molecular dynamics simulation framework

Molecular dynamics simulation is a key method to study protein and other life materials. Due to the great complexity, simulating macromolecule needs huge amounts of calculation and its application is limited. PeerMD, a P2P molecular dynamics simulation framework is proposed. It utilizes free CPU time and network bandwidth of huge amounts of peers to serve large scale molecular dynamics simulation, and uses Web services for interoperating between heterogeneous peers. MDWS, molecular dynamics simulation Web service is defined, method of publishing, discovering and invoking of MDWS based on multi-level SuperPeer is proposed. A protocol system of PeerMD is implemented on JXTA, and experimental simulation of tumor necrosis factor alpha (TNF-alpha) on it shows that PeerMD can speed up molecular dynamics simulation perfectly.