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Molecular Dynamics Simulation on Protein Using Gromacs

Molecular Dynamics Simulation on Protein Using Gromacs

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Published by ijcsis
Development of computer technology in chemistry brings many applications 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. In the molecular dynamics simulation, Gromacs does not work alone. Gromacs interacts 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.
Development of computer technology in chemistry brings many applications 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. In the molecular dynamics simulation, Gromacs does not work alone. Gromacs interacts 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.

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Published by: ijcsis on Mar 08, 2011
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(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
1
, A.B. Mutiara
2
 
Faculty of Computer Science and Information Technology, Gunadarma UniversityJl. Margonda Raya No.100, Depok 16424, Indonesia
 
1,2
{rina,amutiara}@staff.gunadarma.ac.id
Abstract
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.
 
Keywords-
molecular dynamics; Gromac; Pymol; Grace
 
I.
 
I
NTRODUCTION
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.
 
T
HEORIES
 
A.
 
Protein
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).
B.
 
Molecular Dynamics
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) [8].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
C.
 
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,
16 http://sites.google.com/site/ijcsis/ISSN 1947-5500
 
(IJCSIS) International Journal of Computer Science and Information Security,Vol. 9, No. 2, February 2011
even up to hundreds of times. Molecular dynamics procedurecan be described with the flowchart as follows:
Figure 1. Flowchart molecular dynamics [13]
From The figure above can be seen the process of molecular dynamics simulation. The arrow indicates a pathsequence the process will be done. The main process iscalculating forces, computing motion of atoms, and showingstatistical analysis the configuration for each atom.III.
 
G
ROMACS
 
A.
 
Gromacs Concepts
Figure 2. Periodic boundary condition In Two Dimensions [7]
Gromacs is an application that was first developed bydepartment of chemistry in Groningen University. Thisapplication is used to perform molecular dynamics simulationsand energy minimization. The concept used in Gromacs is aperiodic boundary condition and group. Periodic boundarycondition is classical way used in Gromacs to reduce edgeeffect in system. The atom will be placed in a box, surroundedby a copy of the atom.In Gromacs there are some model boxes. That is triclinic,cubic, and octahedron. The second concept is group. Thisconcept is used in Gromacs to show an action. Each group canonly have a maximum number of 256 atoms, where each atomcan only have six different groups.
B.
 
Install Gromacs
Gromacs applications can run on the operating systemLinux and windows. To run Gromacs on multiple computer,then the required MPI (Message Passing Interface) library forparallel communication.Gromacs applications can bedownloaded in http://www.gromacs.org.How to install Gromacs is as follows:1.
 
Download FFTW in http://www.fftw.org2.
 
Extract file FFTW
% tar xzf fftw3-3.0.1.tar.gz% cd fftw3-3.0.1
3.
 
Configuration
%./configure --prefix=/home/anas/fftw3 --enable-float
4.
 
Compile fftw
% make
5.
 
Installing fftw
% make install
6.
 
After fftw installed then install Gromacs. ExtractGromacs.
% Tar xzf gromacs-3.3.1.tar.gz% cd gromacs-3.3.1
7.
 
Configuration
% Export CPPFLAGS =-I/home/anas/fftw3/include% export LDFLAGS=-L/home/anas/fftw3/lib% Export LDFLAGS =-L/home/anas/fftw3/lib%. /configure –prefix=/home/anas/gromacs%. / Configure-prefix = / home / Anas /gromacs
8.
 
Compile and install gromacs
% make & make install
C.
 
Flowchart of Gromacs
Gromacs need several steps to set up a file input in thesimulation. The steps can be seen in flowchart below.Flowchart illustrates how to do molecular dynamics simulationof a protein. The steps are divided into:
17 http://sites.google.com/site/ijcsis/ISSN 1947-5500
 
(IJCSIS) International Journal of Computer Science and Information Security,Vol. 9, No. 2, February 2011
1.
 
Conversion of the pdb fileAt this step pdb is converted to gromos file (gro) withpdb2gmx. Pdbgmx also created topology file (.top)2.
 
Generate boxAt this step, the editconf will determine the type of boxand the box size that will be used in the simulation. onGromacs there are three types of box, namely triclinic,cubic, and octahedron.3.
 
Solvate proteinThe next step is solvate the protein in box. Theprogram genbox will do it. Genbox will generate a boxdefined by editconf based on the type. Genbox alsodetermined the type of water model that will be usedand add number of water molecule for solvate proteinthe water model commonly used is SPC (Simple PointCharge).
Figure 3. Flowchart Gromacs [16].
4.
 
Energy minimizationThe process of adding hydrogen bond or terminationmay cause atoms in protein too close, so that thecollision occurred between the atoms. The collisionbetween atoms can be removed by energyminimization. Gromacs use mdp file for setupparameters. Mdp file specified number of step and cut-off distance. Use grompp to generate input file andmdrun to run energi minimization. The energyminimization may take some time, depending on theCPU [21].5.
 
Molecular dynamics simulationThe process of molecular dynamics simulation is thesame as energy minimization. Grompp prepare theinput file to run mdrun. Molecular dynamicssimulations also need mdp file for setup parameters.Most option of mdrun on molecular dynamics is usedin energy minimization except –x to generate trajectoryfile.6.
 
AnalysisAfter the simulation has finished, the last step is toanalyze the simulation result with the followingprogram:
 
Ngmx to perform trajectory
 
G_energy to monitor energy
 
G_rms to calculated RMSD (root meansquare deviation)
D.
 
File Format 
In Gromacs, there are several types of file format:
 
Trr: a file format that contains data trajectory forsimulation. It stores information about the coordinates,velocities, force, and energy.
 
Edr: a file format that stores information about energiesduring the simulation and energy minimization.
 
Pdb: a form of file format used by Brookhaven proteindata bank. This file contains information about positionof atoms in structure of molecules and coordinatesbased on ATOM and HETATM records.
 
Xvg: a form of file format that can be run by Grace.This file is used to perform data in graphs.
 
Xtc: portable format for trajectory. This file shows thetrajectory data in Cartesian coordinates.
 
Gro: a file format that provides information about themolecular structure in format gromos87. Theinformation displayed in columns, from left to right.
 
Tpr: a binary file that is used as input file in thesimulation. This file can not be read through thenormal editor.
 
Mdp: a file format that allows the user to setup theparameters in simulation or energy minimization.
E.
 
Gromacs Programs1)
 
Pdb2gmx
18 http://sites.google.com/site/ijcsis/ISSN 1947-5500

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