Molecular simulation such as molecular dynamics requires high computing capacity of large scale clusters or supercomputers to complete its experiment. Since it is hard to calculate with general computer, high computing power such as grid computing is required through the web. After the simulation, the result file is created and replicated to the web. To analysis the experiment, biologist has to download it, but large amount of file takes many times to download and analysis the result. We propose a web-based interactive monitoring system for molecular simulation. The grid system is used for computing equations of molecular simulations. The results can be viewed through 3D animations and manipulated by interactive manners. The operations can be performed through web browsers over the Internet. The proposed system was evaluated in performance in comparison with previous approaches. The proposed system enable biologist to analysis the simulation results five times faster than previous tools.