introduction to gaussian packagethe university of north 高斯包對(duì)中北大學(xué)簡(jiǎn)介

1、Introduction to Gaussian and GaussViewShubin Liu, Ph.D.Renaissance Computing InstituteUniversity of North Carolina at Chapel HillAgendaIntroductionCapabilitiesInput File PreparationGaussian GUI GaussViewRun G03 Jobs UNC-CHSome Advanced TopicsHands-on Experiments11/6/20062Introduction to GaussianCour

2、se GoalWhat Gaussian/GaussView packages areHow to prepare input files via GaussView How to run G03 jobs on UNC-CH serversHow to view G03 resultsLearn selected advanced topicsHands-on experiments11/6/20063Introduction to GaussianPre-requisitesBasic UNIX knowledgeIntroduction to Scientific ComputingAn

3、 account on Emerald11/6/20064Introduction to GaussianAbout MyselfPh.D. from Chemistry, UNC-CHCurrently Senior Computational Scientist UNC ITS Research Computing DivisionResponsibilities:Support Comp Chem/Phys/Material Science software, Support Programming (FORTRAN/C/C+) tools, code porting, parallel

4、 computing, etc.Engagement projects with faculty members on campusConduct own research on Comp ChemDFT theory and conceptSystems in biological and material science11/6/20065Introduction to GaussianAbout YouName, department, group, interest?Any experience before with Gaussian or GaussView?What do you

5、 expect to use them? What kind of systems?11/6/20066Introduction to GaussianGaussian & GaussViewGaussian is a general purpose electronic structure package for use in computational chemistry. Current version 03 D02.GaussView is a graphical user interface (GUI) designed to be used with Gaussian to mak

6、e calculation preparation and output analysis easier, quicker and more efficient. Current version 3.0.9.Vendors website: :/gaussian11/6/20067Introduction to GaussianGaussian11/6/20068Introduction to GaussianGaussian 98/03 FunctionalityEnergiesMM: AMBER, Dreiding, UFF force fieldSemiempirical: CNDO,

7、INDO, MINDO/3, MNDO, AM1, PM3HF: closed-shell, restricted/unrestricted open-shellDFT: many local/nonlocal functionals to chooseMP: 2nd-5th order; direct and semi-direct methodsCI: single and doubleCC: single, double, triples contributionHigh accuracy methods: G1, G2, CBS, etc.MCSCF: including CASSCF

8、GVB11/6/20069Introduction to GaussianGaussian 98/03 FunctionalityGradients/Geometry optimizationsFrequencies (IR/Raman, NMR, etc.)Other propertiesPopulations analysesElectrostatic potentialsNMR tensorsSeveral solvation models (PCM, COSMOS)Two and three layer ONIOM E, grad, freqTransition state searc

9、hIRC for reaction path11/6/200610Introduction to GaussianNew in Gaussian 03Molecular DynamicsBOMD Born-Oppenheimer MDADMP Atom-Centered Density Matrix PropagationPeriodic Boundary Conditions (PBC) HF and DFT energies and gradientsProperties with ONIOM modelsSpin-spin coupling and other additions to

10、spectroscopic propertiesAlso improved algorithms for initial guesses in DFT and faster SCF convergence11/6/200611Introduction to GaussianGaussian Input File Structure ,.inp, or .gjf (Windows version)Free format, case insensitiveSpaces, commas, tabs, forward slash as delimiters between keywords! as c

11、omment line/sectionDivided into sections (in order)Link 0 commands (%)Route section what calculation is to doTitleMolecular specificationOptional additional sections11/6/200612Introduction to GaussianInput File Example 1# HF/6-31G(d)!Route section !Blank linewater energy !Title section !Blank line0

12、1 !Charge & multiplicityO -0.464 0.177 0.0 !Geometry in Cartesian CoordinateH -0.464 1.137 0.0 H 0.441 -0.143 0.0 !Blank line11/6/200613Introduction to GaussianInput File Example 2%nproc=2 !Link 0 section%chk=water.chk #b3lyp/6-311+G(3df,2p) opt freq !Route/Keywords !Blank lineCalcn Title: test !Tit

13、le!Ban line0 1 !Charge & multiplicityO!Geometry in Z-matrixh 1 r h 1 r 2 a variablesr=0.98 a=109. !Blank line 11/6/200614Introduction to GaussianInput File Link 0 CommandsFirst “Link 0” options (Examples)%chk%chk=myjob.chk%mem%mem=12MW%nproc $nproc=4%rwf%rwf=1,1999mb,b,1999mb%scr%sc=e,1999mb,f,1999m

14、b11/6/200615Introduction to GaussianInput File Keyword SpecificationKeyword line(s) specify calculation type and other job optionsStart with # symbolCan be multiple linesTerminate with a blank lineFormatkeyword=optionkeyword(option)keyword(option1,option2,)keyword=(option1,option2,)Users guide provi

15、des list of keywords, options, and basis set notion :/gaussian/g_ur/keywords.htm11/6/200616Introduction to Gaussian11/6/200617Introduction to GaussianBasis SetMinimal basis set (e.g., STO-3G)Double zeta basis set (DZ)Split valence basis Set (e.g., 6-31G)Polarization and diffuse functions (6-31+G*)Co

16、rrelation-consistent basis functions (e.g., aug-cc-pvTZ)Pseudopotentials, effective core potentials11/6/200618Introduction to Gaussian11/6/200619Introduction to GaussianInput File Title SpecificationBrief description of calculation for users benefitTerminate with a blank line11/6/200620Introduction

17、to GaussianInput File Molecular Geometry1st line charge and multiplicityElement label and locationCartesian coordinateLabel x y zZ-matrixLabel atoms bond length atom2 angle atm3 dihedralIf parameters used instead of numerical values then variables section followsAgain end in blank line11/6/200621Int

18、roduction to GaussianA More Complicated Example%chk=/scr/APPS_SCRDIR/f33em5p77c.chk%mem=4096MB%NProc=4#B3LYP/6-31G* opt geom=Checkpoint Guess=read nosymm scf=tightGeometry optimization of a sample molecule1 1 -Link1-%chk=/scr/APPS_SCRDIR/f33em5p77c.chk%mem=4096MB%NProc=2# B3LYP/6-311+G* sp pop=nbo n

19、osymm guess=read geom=checkpointSingle Point Energy for the reference state of molecule with one more electron.0 2 11/6/200622Introduction to GaussianOther Gaussian Utilitiesformchk formats checkpoint file so it can be used by other programscubgen generate cube file to look at MOs, densities, gradie

20、nts, NMR in GaussViewfreqchk retrieves frequency/thermochemsitry data from chk filenewzmat converting molecular specs between formats (zmat, cart, chk, cache, frac coord, MOPAC, pdb, and others)11/6/200623Introduction to GaussianGaussView GaussView 3.0.9 makes using Gaussian 03 simple and straightfo

21、rward: Sketch in molecules using its advanced 3D Structure Builder, or load in molecules from standard files. Set up and submit Gaussian 03 jobs right from the interface, and monitor their progress as they run. Examine calculation results graphically via state-of-the-art visualization features: disp

22、lay molecular orbitals and other surfaces, view spectra, animate normal modes, geometry optimizations and reaction paths. Online help: :/gaussian/g_gv/gvtop.htm11/6/200624Introduction to GaussianGaussView Availability Support platforms: IBM RS6000 (AIX 5.1) SGI (IRIX 6.5.3) Intel Pentium II, III, IV

23、/Athlon (IA32) Linux (RedHat 8.0, 9.0; SuSE 8.2, 9.0, 9.1)11/6/200625Introduction to GaussianGaussView: BuildBuild structures by atom, functional group, ring, amino acid (central fragment, amino-terminated and carboxyl-terminated forms) or nucleoside (central fragment, C3-terminated, C5-terminated a

24、nd free nucleoside forms). Show or hide as many builder panels as desired.Define custom fragment libraries.Open PDB files and other standard molecule file formats. Optionally add hydrogen atoms to structures automatically, with excellent accuracy.Graphically examine & modify all structural parameter

25、s.Rotate even large molecules in 3 dimension: translation, 3D rotation and zooming are all accomplished via simple mouse operations. Move multiple molecules in the same window individually or as a group.Adjust the orientation of any molecule display.View molecules in several display modes: wire fram

26、e, tubes, ball and stick or space fill style. Display multiple views of the same structure.Customize element colors and window backgrounds.Use the advanced Clean function to rationalize sketched-in structuresConstrain molecular structure to a specific symmetry (point group).Recompute bonding on dema

27、nd.Build unit cells for 1, 2 and 3 dimensional periodic boundary conditions calculations (including constraining to a specific space group symmetry). Specify ONIOM layer assignments in several simple, intuitive ways: by clicking on the desired atoms, by bond attachment proximity to a specified atom,

28、 by absolute distance from a specified atom, and by PDB file residue.11/6/200626Introduction to GaussianGaussView: Build11/6/200627Introduction to GaussianGaussView: Build11/6/200628Introduction to GaussianGuassView: SetupMolecule specification input is set up automatically.Specify additional redund

29、ant internal coordinates by clicking on the appropriate atoms and optionally setting the value.Specify the input for any Gaussian 03 calculation type. Select the job from a pop-up menu. Related options automatically appear in the dialog.Select any method and basis set from pop-up menus.Set up calcul

30、ations for systems in solution. Select the desired solvent from a pop-up menu.Set up calculations for solids using the periodic boundary conditions method. GaussView specifies the translation vectors automatically.Set up molecule specifications for QST2 and QST3 transition state searches using the B

31、uilders molecule group feature to transform one structure into the reactants, products and/or transition state guess.Select orbitals for CASSCF calculations using a graphical MO editor, rearranging the order and occupations with the mouse.Start and monitor local Gaussian jobs.Start remote jobs via a

32、 custom script.11/6/200629Introduction to GaussianGaussView: Setup11/6/200630Introduction to GaussianGuassView: Showing ResultsShow calculation results summary.Examine atomic changes: display numerical values or color atoms by charge (optionally selecting custom colors).Create surfaces for molecular

33、 orbitals, electron density, electrostatic potential, spin density, or NMR shielding density from Gaussian job results. Display as solid, translucent or wire mesh.Color surfaces by a separate property.Load and display any cube created by Gaussian 03.Animate normal modes associated with vibrational f

34、requencies (or indicate the motion with vectors).Display spectra: IR, Raman, NMR, VCD. Display absolute NMR results or results with respect to an available reference compound.Animate geometry optimizations, IRC reaction path following, potential energy surface scans, and BOMD and ADMP trajectories.P

35、roduce web graphics and publication quality graphics files and printouts. Save/print images at arbitrary size and resolution.Create TIFF, JPEG, PNG, BMP and vector graphics EPS files.Customize element, surface, charge and background colors, or select high quality gray scale output.11/6/200631Introdu

36、ction to GaussianGuassView: Showing Results11/6/200632Introduction to GaussianSurfaces11/6/200633Introduction to GaussianReflection-Absorption Infrared Spectrum of AlQ37521116133813861473158016051600140012008001000Wavenumbers (cm-1)11/6/200634Introduction to GaussianGaussView: VCD (Vibrational Circu

37、lar Dichroism) SpectraGaussView can display a variety of computed spectra, including IR, Raman, NMR and VCD. Here we see the VCD spectra for two conformations of spiropentyl acetate, a chiral derivative of spiropentane. See F. J. Devlin, P. J. Stephens, C. sterle, K. B. Wiberg, J. R. Cheeseman, and

38、M. J. Frisch, J. Org. Chem. 67, 8090 (2002). 11/6/200635Introduction to GaussianGaussView: ONIOMBacteriorhodopsin, set up for an ONIOM calculation (stylized). See T. Vreven and K. Morokuma, “Investigation of the S0-S1 excitation in bacteriorhodopsin with the ONIOM(MO:MM) hybrid method,” Theor. Chem.

39、 Acc. (2003). 11/6/200636Introduction to GaussianGaussian/GaussView UNCInstalled in AFS ISIS package space /afs/isis/pkg/gaussianPackage name: gaussianVersions: 03C02, 03D02 (default version)Type “ipm add gaussian” to subscribe the serviceAvailabilitySGI Altix 3700, cedar/cypress IBM P690, happy/yat

40、taLINUX cluster, LINUX Cluster, (available upon request)Package information available at: ://608211/6/200637Introduction to GaussianAccess GaussViewFrom UNIX workstationType “xhost + ” or “xhost + ”Login to emerald

41、 or happySet display to your local hostInvoke gaussview or gview via LSF interactive queueFrom PC desktop via X-Win32 or SecureCRTDetailed document available at: ://atn/hpc/applications/science/gaussian/access_gv/g03_gv_instructions.htm11/6/200638Introduction to GaussianSubmit G03 Jobs to Ser

42、versTo submit single-CPU G03 jobs to computing servers via LSF:bsub -q qname -m mname g03 input.inpwhere “qname” stands for a queue name, e.g., week, month, etc., “mname” represents a machine name, e.g., cypress, yatta, etc., and “input.inp” denotes the input file prepared manually or via GaussView.

43、 For example:bsub -q week -m cypress g03 input.inpbsub -q month -m yatta g03 input.inpbsub -q idle -R blade g03 input.inp11/6/200639Introduction to GaussianSubmit G03 Jobs to ServersTo submit multiple-CPU G03 jobs via LSF:bsub -q qname -n ncpu -m mname g03 input.inpwhere “qname” stands for a queue n

44、ame, e.g., week, idle, etc., “ncpu” is the number of CPUs requested, e.g., 2 or 4., “mname” represents a machine name, e.g., yatta, cypress, etc., and “input.inp” denotes the input file prepared manually or via GaussView.For examplebsub -q week -n 4 -m cypress g03 input.inpOn Emerald, only serial G0

45、3 is available because G03 is parallelized via OpenMP (for share-memory SMP machines)11/6/200640Introduction to GaussianDefault SettingsTemporary filesYatta/cypress: /scr/APPS_SCRDIREmerald:/tmpMemory Yatta/cypress: 1GBEmerald: 512MBMAXDISKYatta/cypress: 4GBEmerald: 2GB11/6/200641Introduction to Gau

46、ssianAdvanced TopicsPotential energy surfacesTransition state optimizationThermochemistryNMR, VCD, IR/Raman spectraNBO analysisExcited states (UV/visible spectra)Solvent effectPBCONIOM modelABMD, BOMD, etc.11/6/200642Introduction to GaussianPotential Energy SurfacesMany aspects of chemistry can be r

47、educed to questions about potential energy surfaces (PES)A PES displays the energy of a molecule as a function of its geometryEnergy is plotted on the vertical axis, geometric coordinates (e.g bond lengths, valence angles, etc.) are plotted on the horizontal axesA PES can be thought of it as a hilly

48、 landscape, with valleys, mountain passes and peaksReal PES have many dimensions, but key feature can be represented by a 3 dimensional PES11/6/200643Introduction to GaussianModel Potential Energy Surface11/6/200644Introduction to GaussianCalculating PES in Gaussian/GaussViewUse the keyword “scan” T

49、hen change input file properly11/6/200645Introduction to GaussianTransition State Search11/6/200646Introduction to GaussianCalculating Transition States11/6/200647Introduction to GaussianLocating Transition States11/6/200648Introduction to GaussianTS Search in Gaussian11/6/200649Introduction to Gaus

50、sianTS Search inGaussian/GaussView11/6/200650Introduction to Gaussian11/6/200651Introduction to GaussianAnimation of Imaginary FrequencyCheck that the imaginaryfrequency corresponds tothe TS you search for.11/6/200652Introduction to GaussianIntrinsic Reaction Coordinate Scans11/6/200653Introduction

51、to GaussianInput for IRC CalculationStepSize=N Step size along the reaction path, in units of 0.01 amu-1/2-Bohr. The default is 10. RCFC Specifies that the computed force constants in Cartesian coordinates from a frequency calculation are to be read from the checkpoint file. ReadCartesianFC is a syn

52、onym for RCFC. 11/6/200654Introduction to GaussianIRC Calculation in GaussView11/6/200655Introduction to GaussianReaction Pathway Graph11/6/200656Introduction to GaussianThermochemistryfrom ab initio Calculations11/6/200657Introduction to GaussianThermochemistryfrom ab initio Calculations11/6/200658

53、Introduction to GaussianThermochemistry from frequency calculation11/6/200659Introduction to GaussianModeling System in Solution11/6/200660Introduction to GaussianCalculating Solvent Effect11/6/200661Introduction to GaussianCalculating Solvent Effect11/6/200662Introduction to GaussianSolvent Effect:

54、 Menshutkin Model Reaction Transition State11/6/200663Introduction to Gaussian11/6/200664Introduction to GaussianNMR Shielding Tensors11/6/200665Introduction to GaussianNMR Example Input%chk=ethynenmr#p hf/6-311+g(2d,p) nmrnmr ethyne0 1CC,1,r1H,1,r2,2,a2H,2,r3,1,a3,3,d3,0 VariablesR1=1.20756258R2=1.

55、06759666R3=1.06759666A2=180.0A3=180.0D3=0.011/6/200666Introduction to Gaussian11/6/200667Introduction to Gaussian11/6/200668Introduction to GaussianComparison of Calculated and Experimental Chemical Shifts11/6/200669Introduction to GaussianQM/MM: ONIOM Model11/6/200670Introduction to GaussianQM/MM:

56、ONIOM ModelFrom GaussView menu: Edit - Select LayerLow LayerMedium LayerHigh Layer11/6/200671Introduction to GaussianQM/MM: ONIOM SetupFrom GaussView menu: Calculate -Gaussian-Method11/6/200672Introduction to GaussianQM/MM: ONIOM SetupFor the medium and low layers:11/6/200673Introduction to Gaussian

57、QM/MM: ONIOM Setup11/6/200674Introduction to GaussianWhat Is NBO?Natural Bond Orbitals (NBOs) are localized few-center orbitals (few meaning typically 1 or 2, but occasionally more) that describe the Lewis-like molecular bonding pattern of electron pairs (or of individual electrons in the open-shell

58、 case) in optimally compact form. More precisely, NBOs are an orthonormal set of localized maximum occupancy orbitals whose leading N/2 members (or N members in the open-shell case) give the most accurate possible Lewis-like description of the total N-electron density. C-C BondC-H Bond11/6/200675Introduction to GaussianNBO Analysis11/6/200676Introduction to GaussianNBO in GaussView11/6/200677Introduction to GaussianNatural Population Analysis#rhf/3-21g pop=nbo RHF/3-21G for formamide (H2NCH