  Development of computer technology in chemistry, bring many application of
chemistry. Not only the application to visualize the structure of molecule but
also to molecular dynamics simulation. One of them is Gromacs. Gromacs is an
example of molecular dynamics application developed by Groningen University.
This application is a non-commercial and able to work in the operating system
Linux. The main ability of Gromacs is to perform molecular dynamics simulation
and minimization energy. In this paper, the author discusses about how to work
Gromacs in molecular dynamics simulation of some protein. In the molecular
dynamics simulation, Gromacs does not work alone. Gromacs interact with pymol
and Grace. Pymol is an application to visualize molecule structure and Grace is
an application in Linux to display graphs. Both applications will support
analysis of molecular dynamics simulation.
