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Development of computer technology in chemistry, bring many application ofchemistry. Not only the application to visualize the structure of molecule butalso to molecular dynamics simulation. One of them is Gromacs. Gromacs is anexample of molecular dynamics application developed by Groningen University.This application is a non-commercial and able to work in the operating systemLinux. The main ability of Gromacs is to perform molecular dynamics simulationand minimization energy. In this paper, the author discusses about how to workGromacs in molecular dynamics simulation of some protein. In the moleculardynamics simulation, Gromacs does not work alone. Gromacs interact with pymoland Grace. Pymol is an application to visualize molecule structure and Grace isan application in Linux to display graphs. Both applications will supportanalysis of molecular dynamics simulation.

Performance Analysis on Molecular Dynamics Simulation of Protein Using GROMACS