Introduction To GaussView And Gaussian

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Introduction toGaussView and GaussianBenjamin J. .eduwww.msi.umn.edu

Description of Both ProgramsHow to Create Input Files (with GaussView)How to Submit CalculationsHow to Visualize OutputDescription Input Submit Visualizewww.msi.umn.edu

Gaussian 03:an electronic structure package capable of predicting manyproperties of atoms, molecules, and reactive systemse.g. Energies Structures Vibrational frequenciesutilizing ab initio, density functional theory, semi-empirical,molecular mechanics, and hybrid methods.Description Input Submit Visualizewww.msi.umn.edu

GaussView:graphical interface for Gaussian 03 build molecules or reactive systems setup Gaussian 03 input files graphically examine resultsDescription Input Submit Visualizewww.msi.umn.edu

GaussViewVisualizationInput/OutputText FilesGaussian03Electronic Structure CalculationsDescription Input Submit Visualizewww.msi.umn.edu

Calculations with GaussianDescription Input Submit Visualizewww.msi.umn.edu

Types of Calculations single point energy and properties (electrondensity, dipole moment, ) geometry optimization frequency reaction path followingDescription Input Submit Visualizewww.msi.umn.edu

Levels of Theory Available:– semi-empiricalAM1, PM3, MNDO, – density functional theoryB3LYP, MPW1PW91, – ab initioThe level of theory is theset of underlying approximationsused to describe the chemicalsystem. Higher levels of theoryare often more accurate howeverthey come at much greatercomputational cost.HF, MP2, CCSD, CCSD(T), – hybridG2, G3, Description Input Submit Visualizewww.msi.umn.edu

Basis Sets Available:– Pople-type3-21G, 6-31G, 6-311G(d,p), – Dunningcc-pVDZ, aug-cc-pVTZ, Basis sets are used for mostcalculations in Gaussian. Theyare a set of functions that areused to describe electronicwavefunctions.– Huzinaga and OthersMIDIX, – User-definedDescription Input Submit Visualizewww.msi.umn.edu

Creating Input Files for GaussianDescription Input Submit Visualizewww.msi.umn.edu

Water Optimization Input File%mem 32mb#p hf/6-31g optsystem resourcescomputational modeltype of calculationhf/6-31g optimization of watertitle0 1oh 1 ohh 1 oh 2 ahohcharge & multiplicityoh 0.9ahoh 104.0structure definition(z-matrix)variable valuesDescription Input Submit Visualizewww.msi.umn.edu

Spin multiplicity:multiplicity n 1where n # of unpaired electronsDescription Input Submit Visualizewww.msi.umn.edu

Building with GaussView: Instead of typing all the coordinates, theory, basisset, etc., we can use GaussView. The calculation is specified by pointing and clickingto build the molecule, and using pull-down menus toselect the calculation type, level of theory and basisset. GaussView generates the Gaussian input file, andcan run Gaussian without ever returning to the Unixprompt. GaussView can also be used to read Gaussianoutput files and visualize the results.Description Input Submit Visualizewww.msi.umn.edu

Getting Started with GaussView: Login remotelyssh -X sp.msi.umn.edu Load Gaussian/GaussView modulemodule add g03 Launch GaussViewgvDescription Input Submit Visualizewww.msi.umn.edu

BuilderViewerDescription Input Submit Visualizewww.msi.umn.edu

Mouse ButtonLeftCenter/Left-RightRightActionClickDrag Left/RightDrag Up/DownDragFunctionSelects or inserts itemRotates about Y-axisRotates about X-axisTranslation ofmoleculeDrag Left/Right Rotates about Z-axisDrag Up/Down Zooms in and outNote: Holding down the Tab key limits mouse action to the closestdistinct fragment.Description Input Submit Visualizewww.msi.umn.edu

MoleculeBuildingSelected fragmentsAre previewed hereFragments areSelectedMolecule is put togetherHereDescription Input Submit Visualizewww.msi.umn.edu

MoleculeBuildingThe atom labeled “Hot” is is where the fragmentwill attach to the system you are building.Description Input Submit Visualizewww.msi.umn.edu

Steps to Building Choose an atom or fragment Choose the location of the fragment thatwill attach to your molecule in the builderwindow Select/add the fragment to your moleculein the viewer window repeatwww.msi.umn.edu

Elements:Description Input Submit Visualizewww.msi.umn.edu

Ring Fragments:Description Input Submit Visualizewww.msi.umn.edu

R-Group Fragments:Description Input Submit Visualizewww.msi.umn.edu

Biological Fragments:Description Input Submit Visualizewww.msi.umn.edu

MoleculeBuildingclean upThis option will use a MMcalculation to optimize thegeometry (very fast).Description Input Submit Visualizewww.msi.umn.edu

Submitting CalculationsDescription Input Submit Visualizewww.msi.umn.edu

Interactive:Command:g03 input file output fileNotes:1) input and output files can use absolute or relativepathnames2) Gaussian temporary files can be redirected bysetting the GAUSS SCRDIR environment variable.setenv GAUSS SCRDIR /scratch/pfast3) BE CAREFUL how long you run interactivelyDescription Input Submit Visualizewww.msi.umn.edu

Batch:Command:qg03 [-options] input fileOptions:-h-e-m-n-p-r-s-thelp, display a usage list and the defaultsemail notificationtotal amount of memorynode, choose the particular processornumber of processorsrun?scratch spaceamount of wallclock timeDescription Input Submit Visualizewww.msi.umn.edu

Select GaussianSubmitting jobs through GaussView:Description Input Submit Visualizewww.msi.umn.edu

Choose Job TypeDescription Input Submit Visualizewww.msi.umn.edu

Method & Basis SetDescription Input Submit Visualizewww.msi.umn.edu

Save Input FileDescription Input Submit Visualizewww.msi.umn.edu

Description Input Submit Visualizewww.msi.umn.edu

Description Input Submit Visualizewww.msi.umn.edu

The submissiondialogue box will appeara little different dependingon which machine youare running GaussView on.Description Input Submit Visualizewww.msi.umn.edu

Submitting your Gaussian jobIf you haven’t saved your input file yet, Gaussview willPrompt you to save your input file.You will name the input file, and then submit the calculation.When Gaussian is finished running, you will receive a messagein Gaussview.Description Input Submit Visualizewww.msi.umn.edu

How to VisualizeDescription Input Submit Visualizewww.msi.umn.edu

Visualization FeaturesDescription Input Submit Visualizewww.msi.umn.edu

How to view your output Your submitted calculation will run in thebackground. When it is complete, Gaussview willinform you and ask you if you wish toview an output file. From the list of files, you can pick youroutput (something.chk)www.msi.umn.edu

How to view your output If you ever want to open an output fileagain, you can go to:File OpenIn the GaussView menus to open any outputfile.www.msi.umn.edu

Output that can be visualized Geometry Vibrations Orbitals Electron density Electrostatic potentialwww.msi.umn.edu

Main results menuDescription Input Submit Visualizewww.msi.umn.edu

FrequenciesDescription Input Submit Visualizewww.msi.umn.edu

SpectraDescription Input Submit Visualizewww.msi.umn.edu

A cube file is aformat of 3-Ddata that canbe plotted.You can generatea cube file to displayorbitals, electrondensities, electrostaticpotentials, etc.www.msi.umn.edu

Description Input Submit Visualizewww.msi.umn.edu

Questions?http://www.gaussian.comemail: .eduDescription Input Submit Visualizewww.msi.umn.edu

to build the molecule, and using pull-down menus to select the calculation type, level of theory and basis set. GaussView generates the Gaussian input file, and can run Gaussian without ever returning to the Unix prompt. GaussView can also be used to read Gaussian output files and visualize the results. Description Input Submit .

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