Gaussian GaussView

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Agenda. IntroductionCapabilitiesInput File PreparationGaussian GUI GaussViewRun G03/G09 Jobs @ UNC-CHSome Advanced TopicsHands-on Experiments next hour. The PPT format of this presentation is available here:http://its2.unc.edu/divisions/rc/training/scientific//afs/isis/depts/its/public_
Gaussian GaussView

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1. Gaussian & GaussView Shubin Liu, Ph.D. Research Computing Center, ITS University of North Carolina at Chapel Hill The Title Slide: Add the name of the presentation, the appropriate division or presenter and date of the presentation.The Title Slide: Add the name of the presentation, the appropriate division or presenter and date of the presentation.

2. Agenda Introduction Capabilities Input File Preparation Gaussian GUI ? GaussView Run G03/G09 Jobs @ UNC-CH Some Advanced Topics Hands-on Experiments ? next hour

3. Course Goal What Gaussian/GaussView packages are How to prepare input files via GaussView How to run G03/G09 jobs on UNC-CH servers How to view G03/G09 results Learn selected advanced topics Hands-on experiments

4. Pre-requisites Basic UNIX knowledge Introduction to Scientific Computing An account on Emerald

5. About Us ITS ? Information Technology Services http://its.unc.edu http://help.unc.edu Physical locations: 401 West Franklin St. 211 Manning Drive 10 Divisions/Departments Information Security IT Infrastructure and Operations Research Computing Center Teaching and Learning User Support and Engagement Office of the CIO Communication Technologies Communications Enterprise Applications Finance and Administration

6. Research Computing Center Where and who are we and what do we do? ITS Manning: 211 Manning Drive Website http://its.unc.edu/research-computing.html Groups Infrastructure -- Hardware User Support -- Software Engagement -- Collaboration

7. About Myself Ph.D. from Chemistry, UNC-CH Currently Senior Computational Scientist @ Research Computing Center, UNC-CH Responsibilities: Support Computational Chemistry/Physics/Material Science software Support Programming (FORTRAN/C/C++) tools, code porting, parallel computing, etc. Training, Workshops/Short Courses ? currently 4, one more to come soon Conduct research and engagement projects in Computational Chemistry Development of DFT theory and concept tools Applications in biological and material science systems

8. About You Name, department, group, interest? Any experience before with Gaussian or GaussView? What do you expect to use them? What kind of systems?

9. Gaussian & GaussView Gaussian is a general purpose electronic structure package for use in computational chemistry. Current default version 03 E01 Most widely used computational chemistry package. The latest release is Gaussian 09A02. GaussView is a graphical user interface (GUI) designed to be used with Gaussian to make calculation preparation and output analysis easier, quicker and more efficient. Current default version 4.1.2. The latest release is 5.0.9. Vendor?s website: http://www.gaussian.com

11. Gaussian 03/09 Functionality Energies MM: AMBER, Dreiding, UFF force field Semiempirical: CNDO, INDO, MINDO/3, MNDO, AM1, PM3 HF: closed-shell, restricted/unrestricted open-shell DFT: many local/nonlocal functionals to choose MP: 2nd-5th order; direct and semi-direct methods CI: single and double CC: single, double, triples contribution High accuracy methods: G1, G2, CBS, etc. MCSCF: including CASSCF GVB

12. Gaussian 03/09 Functionality Gradients/Geometry optimizations Frequencies (IR/Raman, NMR, etc.) Other properties Populations analyses Electrostatic potentials NMR tensors Several solvation models (PCM, COSMOS) Two and three layer ONIOM ? E, grad, freq Transition state search IRC for reaction path

13. New in Gaussian 03/09 Molecular Dynamics BOMD ? Born-Oppenheimer MD ADMP ? Atom-Centered Density Matrix Propagation Periodic Boundary Conditions (PBC) ? HF and DFT energies and gradients Properties with ONIOM models Spin-spin coupling and other additions to spectroscopic properties Also ? improved algorithms for initial guesses in DFT and faster SCF convergence Many new DFT functionals! DFTB (tight-binding DFT)

14. Gaussian Input File Structure .com,.inp, or .gjf (Windows version) Free format, case insensitive Spaces, commas, tabs, forward slash as delimiters between keywords ! as comment line/section Divided into sections (in order) Link 0 commands (%) Route section ? what calculation is to do Title Molecular specification Optional additional sections

15. Input File ? Example 1 # HF/6-31G(d) !Route section !Blank line water energy !Title section !Blank line 0 1 !Charge & multiplicity O -0.464 0.177 0.0 !Geometry in Cartesian Coordinate H -0.464 1.137 0.0 H 0.441 -0.143 0.0 !Blank line at the end

16. Input File ? Example 2 %nproc=2 !Link 0 section %chk=water.chk #b3lyp/6-311+G(3df,2p) opt freq !Route/Keywords !Blank line Calcn Title: test !Title !Ban line 0 1 !Charge & multiplicity O !Geometry in Z-matrix h 1 r h 1 r 2 a variables r=0.98 a=109. !Blank line at the end

17. Input File ? Link 0 Commands First ?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,1999mb

18. Input File ? Keyword Specification Keyword line(s) ? specify calculation type and other job options Start with # symbol Can be multiple lines Terminate with a blank line Format keyword=option keyword(option) keyword(option1,option2,?) keyword=(option1,option2,?) User?s guide provides list of keywords, options, and basis set notion http://www.gaussian.com/g_ur/keywords.htm

21. Basis Set Why are basis sets required: MO-LCAO! Basis sets are atomic orbitals (AOs). Minimal 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*) Correlation-consistent basis functions (e.g., aug-cc-pvTZ) Pseudopotentials, effective core potentials

23. Input File ? Title Specification Brief description of calculation ? for users benefit Terminate with a blank line

24. Input File ? Molecular Geometry 1st line charge and multiplicity Element label and location Cartesian coordinate Label x y z Z-matrix Label atoms bond length atom2 angle atm3 dihedral If parameters used instead of numerical values then variables section follows Again end in blank line

25. A More Complicated Example

26. Other Gaussian Utilities formchk ? formats checkpoint file so it can be used by other programs cubgen ? generate cube file to look at MOs, densities, gradients, NMR in GaussView freqchk ? retrieves frequency/thermochemsitry data from chk file newzmat ? converting molecular specs between formats (zmat, cart, chk, cache, frac coord, MOPAC, pdb, and others)

27. GaussView GaussView 4.1.2 makes using Gaussian 03 simple and straightforward: 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: display molecular orbitals and other surfaces, view spectra, animate normal modes, geometry optimizations and reaction paths. Online help: http://www.gaussian.com/g_gv/gvtop.htm

28. GaussView Availability Support platforms: ? IBM RS6000 (AIX 5.1) (Happy/yatta/p575) ? LINUX 32-bit OS (Emeraldtest) ? LINUX 64-bit OS (Emerald, Topsail, Kure)

29. GaussView: Build Build structures by atom, functional group, ring, amino acid (central fragment, amino-terminated and carboxyl-terminated forms) or nucleoside (central fragment, C3?-terminated, C5?-terminated and 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 parameters. 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 frame, 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 structures Constrain molecular structure to a specific symmetry (point group). Recompute bonding on demand. 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, by absolute distance from a specified atom, and by PDB file residue.

30. GaussView: Build

31. GaussView: Build

32. GuassView: Setup Molecule specification input is set up automatically. Specify additional redundant 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 calculations 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 Builder?s 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 custom script.

33. GaussView: Setup

34. GuassView: Showing Results Show calculation results summary. Examine atomic changes: display numerical values or color atoms by charge (optionally selecting custom colors). Create surfaces for molecular 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 frequencies (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. Produce 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.

35. GuassView: Showing Results

36. Surfaces

37. Reflection-Absorption Infrared Spectrum of AlQ3 - begining to look at some organic semiconductors - very good agreement with ALQ3 - an electron transport material - so many bands that intensities are essential for identifying peaks- begining to look at some organic semiconductors - very good agreement with ALQ3 - an electron transport material - so many bands that intensities are essential for identifying peaks

38. GaussView: VCD (Vibrational Circular Dichroism) Spectra

39. GaussView: ONIOM

40. Gaussian/GaussView @ UNC Installed in AFS ISIS package space /afs/isis/pkg/gaussian Package name: gaussian Versions: 09A02, 03E01 (default version) Type ?ipm add gaussian? to subscribe the service Availability Linux Cluster, kure.isis.unc.edu LINUX cluster, emerald.isis.unc.edu LINUX Cluster, topsail.unc.edu Package information available at: http://help.unc.edu/6082

41. Access GaussView From UNIX workstation Login to emerald, kure, topsail ssh -X emerlad.isis.unc.edu Invoke gaussview or gview via LSF interactive queue From PC desktop via X-Win32 or SecureCRT Detailed document available at: http://its2.unc.edu/divisions/rc/training/scientific/g03_gv_instructions.doc

42. Submit G03 Jobs to Servers To submit single-CPU G03 jobs to computing servers via LSF: bsub -q qname -m mname g03 input.inp where ?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. For example: bsub -q idle -R blade g03 input.inp

43. Submit G03 Jobs to Servers To submit multiple-CPU G03 jobs via LSF: -- G03 is parallelized via OpenMP bsub -q qname -n ncpu -m mname g03 input.inp where ?qname? stands for a queue name, e.g., week, idle, etc., ?ncpu? is the number of CPUs requested, e.g., 2 or 4 or 8, ?mname? represents a machine name, e.g., yatta, cypress, etc., and ?input.inp? denotes the input file prepared manually or via GaussView. For example bsub -q week -n 4 -m cypress g03 input.inp To submit multiple CPU g03 jobs on Emerald, make sure only all CPUs are from the same node because G03 is parallelized via OpenMP (for share-memory SMP machines) bsub -q week -n 4 -R ?blade span[ptile=4]? g03 input.inp

44. Default Settings Temporary files Emerald: /largefs/gausswork Memory Emerald: 512MB MAXDISK Emerald: 2GB

45. Advanced Topics Potential energy surfaces Transition state optimization Thermochemistry NMR, VCD, IR/Raman spectra NBO analysis Excited states (UV/visible spectra) Solvent effect PBC ONIOM model ABMD, BOMD, etc.

46. Potential Energy Surfaces Many aspects of chemistry can be reduced to questions about potential energy surfaces (PES) A PES displays the energy of a molecule as a function of its geometry Energy is plotted on the vertical axis, geometric coordinates (e.g bond lengths, valence angles, etc.) are plotted on the horizontal axes A PES can be thought of it as a hilly landscape, with valleys, mountain passes and peaks Real PES have many dimensions, but key feature can be represented by a 3 dimensional PES

47. Model Potential Energy Surface

48. Calculating PES in Gaussian/GaussView Use the keyword ?scan? Then change input file properly

49. Transition State Search

50. Calculating Transition States

51. Locating Transition States

52. TS Search in Gaussian

53. TS Search in Gaussian/GaussView

55. Animation of Imaginary Frequency Check that the imaginary frequency corresponds to the TS you search for.

56. Intrinsic Reaction Coordinate Scans

57. Input for IRC Calculation

58. IRC Calculation in GaussView

59. Reaction Pathway Graph

60. Thermochemistry from ab initio Calculations

61. Thermochemistry from ab initio Calculations

62. Thermochemistry from frequency calculation

63. Modeling System in Solution

64. Calculating Solvent Effect

65. Calculating Solvent Effect

66. Solvent Effect: Menshutkin Model Reaction Transition State

68. NMR Shielding Tensors

69. NMR Example Input

72. Comparison of Calculated and Experimental Chemical Shifts

73. QM/MM: ONIOM Model

74. QM/MM: ONIOM Model From GaussView menu: Edit -> Select Layer

75. QM/MM: ONIOM Setup From GaussView menu: Calculate ->Gaussian->Method

76. QM/MM: ONIOM Setup For the medium and low layers:

77. QM/MM: ONIOM Setup

78. What 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 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.

79. NBO Analysis

80. NBO in GaussView

81. Natural Population Analysis #rhf/3-21g pop=nbo RHF/3-21G for formamide (H2NCHO) 0 1 ??H??-1.908544????? 0.420906?????0.000111 ??H??-1.188060???? -1.161135?????0.000063 ??N??-1.084526???? -0.157315?????0.000032 ??C???0.163001????? 0.386691????-0.000154 ??O???1.196265???? -0.246372?????0.000051 ??H???0.140159????? 1.492269?????0.000126

83. Further Readings Computational Chemistry (Oxford Chemistry Primer) G. H. Grant and W. G. Richards (Oxford University Press) Molecular Modeling ? Principles and Applications, A. R. Leach (Addison Wesley Longman) Introduction to Computational Chemistry, F. Jensen (Wiley) Essentials of Computational Chemistry ? Theories and Models, C. J. Cramer (Wiley) Exploring Chemistry with Electronic Structure Methods, J. B. Foresman and A. Frisch (Gaussian Inc.) Pass around copies of the texts We can get the book store to order some if there is enough demand Most will need to buy Exploring Chemistry ? we need to order that directly from GaussianPass around copies of the texts We can get the book store to order some if there is enough demand Most will need to buy Exploring Chemistry ? we need to order that directly from Gaussian

84. Comments & Questions??? In order for create a section divider slide, add a new slide, select the ?Title Only? Slide Layout and apply the ?Section Divider? master from the Slide Design menu. For more information regarding slide layouts and slide designs, please visit http://office.microsoft.com/trainingIn order for create a section divider slide, add a new slide, select the ?Title Only? Slide Layout and apply the ?Section Divider? master from the Slide Design menu. For more information regarding slide layouts and slide designs, please visit http://office.microsoft.com/training

85. Hands-on: Part I Access GaussView to Emerald cluster from PC desktop If not done so before, type ?ipm add gaussian? Check if Gaussian is subscribed by typing ?ipm q? Get to know GaussView GUI Build a simple molecular model Generate an input file for G03 called, for example, input.com View and modify the G03 input file Submit G03 job to emerald compute nodes using the week or now queue: bsub ?R blade ?q now g03 input.com

86. Hands-on: Part II Calculate/View Molecular Orbitals with GaussView http://educ.gaussian.com/visual/Orbs/html/OrbsGaussView.htm Calculate/View Electrostatic Potential with GaussView http://educ.gaussian.com/visual/ESP/html/ESPGaussView.htm Calculate/View Vibrational Frequencies in GaussView http://educ.gaussian.com/visual/Vibs/html/VibsGaussview.htm Calculate/View NMR Tensors with GaussView http://educ.gaussian.com/visual/NMR/html/NMRGausview.htm Calculate/View a Reaction Path with GaussView http://educ.gaussian.com/visual/RPath/html/RPathGaussView.htm


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