A Grid Computing Framework for Large Scale Molecular Dynamics Simulations

Molecular Dynamics(MD) is computational study through simulating in detail the interatomic interactions in protein. Currently, there is no better simulating algorithm due to the demand on accuracy. However, a ensemble/distributed dynamics method is developed to run the simulation in parallel on many distributed computers on the internet. The objective of this research is to design and code a reliable framework to run molecular dynamics computing in a distributed environment ,to make use of the contributed CPU time better and to fasten the computing process of computing. We have sucessfully implemented the framework with Web Service and Java, and have extended this framework transparent to applications for further use on our grid computing environment. The experiments demonstrated that the MD simulation will successfully run on this framework.