Distributed Grid Computing Framework and Application in Molecular Dynamics Simulation
Molecular dynamics performs simulation of the interactions between large number of atoms in the molecular of protein.The time of the folding process of protein is number of 10~(-6) second,while the time step of the simulation is the number of 10~(-15) second,and in every step,computing large amount(O(n~2),n is the number of atoms)of interaction is needed.Therefore,the overall folding process cannot be simulated.No better algorithm can match the requirement of precision.The biologist then develop a distributed process of dynamics, leveraging the computing resources on the internet to make parallel simulation. The goal of this paper is to design and develop a reliable simulation framework for molecular dynamics in various environment such as the P2P and the Grid environment.It can utilize computing resources on a higher level and fasten the computing.We have implemented such framework based on Java and Web services technology and deployed it to our Grid platform.The experiment shows that the simulation program runs well in this framework.