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One of application that needs high performance computing resources ismolecular d ynamic. There is some software available that perform moleculardynamic, one of these is a well known GROMACS. Our previous experimentsimulating molecular dynamics of Indonesian grown herbal compounds showsufficient speed up on 32 n odes Cluster computing environment. In order toobtain a reliable simulation, one usually needs to run the experiment on thescale of hundred nodes. But this is expensive to develop and maintain. Sincethe invention of Graphical Processing Units that is also useful for generalprogramming, many applications have been developed to run on this. This paperreports our experiments that evaluate the performance of GROMACS that runs ontwo different environment, Cluster computing resources and GPU based PCs. Werun the experiment on BRV-1 and REM2 compounds. Four different GPUs areinstalled on the same type of PCs of quad cores; they are Gefore GTS 250, GTX465, GTX 470 and Quadro 4000. We build a cluster of 16 nodes based on thesefour quad cores PCs. The preliminary experiment shows that those run on GTX 470is the best among the other type of GPUs and as well as the cluster computingresource. A speed up around 11 and 12 is gained, while the cost of computerwith GPU is only about 25 percent that of Cluster we built.

Performance Analysis Cluster and GPU Computing Environment on Molecular Dynamic Simulation of BRV-1 and REM2 with GROMACS