One of application that needs high performance computing resources is molecular d ynamic. There is some software available that perform molecular dynamic, one of these is a well known GROMACS. Our previous experiment simulating molecular dynamics of Indonesian grown herbal compounds show sufficient speed up on 32 n odes Cluster computing environment. In order to obtain a reliable simulation, one usually needs to run the experiment on the scale of hundred nodes. But this is expensive to develop and maintain. Since the invention of Graphical Processing Units that is also useful for general programming, many applications have been developed to run on this. This paper reports our experiments that evaluate the performance of GROMACS that runs on two different environment, Cluster computing resources and GPU based PCs. We run the experiment on BRV-1 and REM2 compounds. Four different GPUs are installed on the same type of PCs of quad cores; they are Gefore GTS 250, GTX 465, GTX 470 and Quadro 4000. We build a cluster of 16 nodes based on these four quad cores PCs. The preliminary experiment shows that those run on GTX 470 is the best among the other type of GPUs and as well as the cluster computing resource. A speed up around 11 and 12 is gained, while the cost of computer with GPU is only about 25 percent that of Cluster we built.