(IJCSIS) International Journal of Computer Science and Information Security,Vol. 9, No. 2, February 2011
Molecular Dynamics Simulation on Protein UsingGromacs
A.D. Astuti, R. Refianti
, A.B. Mutiara
Faculty of Computer Science and Information Technology, Gunadarma UniversityJl. Margonda Raya No.100, Depok 16424, Indonesia
Development of computer technology in chemistrybrings many applications of chemistry, not only the application tovisualize the structure of molecule but also to moleculardynamics simulation. One of them is Gromacs. Gromacs is anexample of molecular dynamics application developed byGroningen University. This application is a non-commercial andable to work in the operating system Linux. The main ability of Gromacs is to perform molecular dynamics simulation andminimization energy. In this paper, the author discusses abouthow to work Gromacs in molecular dynamics simulation. In themolecular dynamics simulation, Gromacs does not work alone.Gromacs interacts with Pymol and Grace. Pymol is anapplication to visualize molecule structure and Grace is anapplication in Linux to display graphs. Both applications willsupport analysis of molecular dynamics simulation.
molecular dynamics; Gromac; Pymol; Grace
Computer is necessary for life of society, especially inchemistry. Now, many non-commercial application of chemistry is available in Windows version and also Linux.The applications are very useful not only in visualizationmolecule structure but also to molecular dynamics simulation.Molecular dynamics is a simulation method with computerwhich allowed representing interaction molecules of atom incertain time period. Molecular dynamics technique is based onNewton law and classic mechanics law. Gromacs is one of application which able to do molecular dynamics simulationbased on equation of Newton law. Gromacs was firstintroduced by Groningen University as molecular dynamicssimulation machine.This paper is focused at usage of Gromacs application. Inthis paper, we tell about how to install Gromacs, Gromacsconcepts, file format in Gromacs, Program in Gromacs, andanalysis result of simulation.II.
Protein is complex organic compound that has a highmolecular weight. Protein is also a polymer of amino acid thathas been linked to one another with a peptide bond.Structure of protein divided into three, namely the structureof primary, secondary, tertiary and quaternary. Primarystructure is amino acid sequence of a protein linked to itthrough a peptide bond.Secondary structure is a three-dimensional structure of localrange of amino acids in a protein stabilized by hydrogen bond.Tertiary structure is a combination of different secondarystructures that produce three-dimensional form. Tertiarystructure is usually a lump. Some of the protein molecule caninteract physically without covalent bonds to form a stableoligomer (e.g. dimer, trimer, or kuartomer) and form aQuaternary structure (e.g. rubisco and insulin).
Molecular dynamics is a method to investigate exploringstructure of solid, liquid, and gas. Generally, moleculardynamics use equation of Newton law and classical mechanics.Molecular dynamics was first introduced by Alder andWainwright in the late 1950s, this method is used to study theinteraction hard spheres. From these studies, they learn aboutbehavior of simple liquids. In 1964, Rahman did the firstsimulations using realistic potential for liquid argon. And in1974, Rahman and Stillinger performed the first moleculardynamics simulations using a realistic system that is simulationof liquid water. The first protein simulations appeared in 1977with the simulation of the bovine pancreatic trypsin inhibitor(BPTI) .The main purposes of the molecular dynamics simulationare:
Generate trajectory molecules in the limited timeperiod.
Become the bridge between theory and experiments.
Allow the chemist to make simulation that can’t bodone in the laboratory
The Concepts of Molecular Dynamics
In molecular dynamics, force between molecules iscalculated explicitly and the motion of is computed withintegration method. This method is used to solve equation of Newton in the constituents atomic. The starting condition is theposition and velocities of atoms. Based on Newton’sperception, from starting position, it is possible to calculate thenext position and velocities of atoms at a small time intervaland force in the new position. This can be repeated many times,
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