1. Introduction to Gaussian & GaussView
11/13/2008
Introduction to Gaussian & GaussView
The Title Slide: Add the name of the presentation, the appropriate division or presenter and date of the presentation.
Shubin Liu, Ph.D.
Research Computing Center, ITS
University of North Carolina at Chapel Hill
Research Computing Center, ITS

2. Agenda Introduction Capabilities Input File Preparation
Gaussian & GaussView
Agenda
11/13/2008
Introduction
Capabilities
Input File Preparation
Gaussian GUI – GaussView
Run G03 UNC-CH
Some Advanced Topics
Hands-on Experiments – next hour
The PDF format of this presentation is available here:
Research Computing Center, ITS

3. Course Goal What Gaussian/GaussView packages are
How to prepare input files via GaussView
How to run G03 jobs on UNC-CH servers
How to view G03 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
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
Groups
Infrastructure -- Hardware
User Support -- Software
Engagement -- Collaboration

7. About Myself Ph.D. from Chemistry, UNC-CH
Gaussian & GaussView
Intro to Scientific Computing
About Myself
9/25/20089/11/2008
10/9/2008
11/13/2008
Ph.D. from Chemistry, UNC-CH
Currently Senior Computational 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
Research Computing Center, ITS
Research Computing Center, ITS 7 7

8. Gaussian & GaussView
Gaussian is a general purpose electronic structure package for use in computational chemistry. Current version 03 E01.
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 version
Vendor’s website:

10. Gaussian 98/03 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

11. Gaussian 98/03 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

12. New in Gaussian 03 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

13. Gaussian Input File Structure
Gaussian & GaussView
Gaussian Input File Structure
11/13/2008
.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
Research Computing Center, ITS

14. Input File – Example 1 # HF/6-31G(d) !Route section !Blank line
water energy !Title section
!Charge & multiplicity
O !Geometry in Cartesian Coordinate H H

15. 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
!Charge & multiplicity
O !Geometry in Z-matrix
h 1 r
h 1 r 2 a
variables
r=0.98
a=109.
!Blank line

16. 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

17. 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

19. Basis Set 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

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

22. 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

23. A More Complicated Example
Gaussian & GaussView
A More Complicated Example
11/13/2008
%chk=/scr/APPS_SCRDIR/f33em5p77c.chk
%mem=4096MB
%NProc=4
#B3LYP/6-31G* opt geom=Checkpoint Guess=read nosymm scf=tight
Geometry optimization of a sample molecule
1 1
--Link1--
%NProc=2
# B3LYP/ G** sp pop=nbo nosymm guess=read geom=checkpoint
Single Point Energy for the "reference state" of molecule with one more electron.
0 2
Research Computing Center, ITS

24. 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)

25. GaussView
GaussView 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:

26. GaussView Availability
Support platforms:
– IBM RS6000 (AIX 5.1) (Happy/yatta/p575)
– LINUX 32-bit OS (Emeraldtest)
– LINUX 64-bit OS (Emerald, Topsail, Cedar/Cypress)

27. 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.

28. GaussView: Build

29. GaussView: Build

30. 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.

31. GaussView: Setup

32. 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.

33. GuassView: Showing Results

34. Surfaces

35. Reflection-Absorption Infrared Spectrum of AlQ3
Gaussian & GaussView
Reflection-Absorption Infrared Spectrum of AlQ3
11/13/2008
Wavenumbers (cm-1)
1473
752
- 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
1386
1116
1338
1580
1605
800
1000
1200
1400
1600
Research Computing Center, ITS

36. GaussView: VCD (Vibrational Circular Dichroism) Spectra
GaussView 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. Österle, K. B. Wiberg, J. R. Cheeseman, and M. J. Frisch, J. Org. Chem. 67, 8090 (2002).

37. GaussView: ONIOM
Bacteriorhodopsin, 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. Acc. (2003).

38. Gaussian/GaussView @ UNC
Installed in AFS ISIS package space /afs/isis/pkg/gaussian
Package name: gaussian
Versions: 03D02, 03E01 (default version)
Type “ipm add gaussian” to subscribe the service
Availability
SGI Altix 3700, cedar/cypress
IBM P690, happy/yatta
LINUX cluster, emerald.isis.unc.edu
LINUX Cluster, topsail.unc.edu (available upon request)
Package information available at:

39. Access GaussView From UNIX workstation
Type “xhost + emerald.isis.unc.edu” or “xhost + happy.isis.unc.edu”
Login to emerald, cedar, topsail, or happy
Set display to your local host
Invoke gaussview or gview via LSF interactive queue
From PC desktop via X-Win32 or SecureCRT
Detailed document available at:

40. 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 week -m cypress g03 input.inp
bsub -q month -m p575-n02 g03 input.inp
bsub -q idle -R blade g03 input.inp

41. 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

42. Default Settings Temporary files P575/Yatta/cypress: /scr/APPS_SCRDIR
Emerald: /tmp
Memory
P575/Yatta/cypress: 1GB
Emerald: MB
MAXDISK
P575/Yatta/cypress: 4GB
Emerald: GB

43. 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.

44. 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

45. Model Potential Energy Surface
Gaussian & GaussView
Model Potential Energy Surface
11/13/2008
Research Computing Center, ITS

46. Calculating PES in Gaussian/GaussView
Use the keyword “scan”
Then change
input file properly

47. Transition State Search

48. Calculating Transition States

49. Locating Transition States

50. TS Search in Gaussian

51. TS Search in Gaussian/GaussView

52. TS Search in Gaussian/GaussView

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

54. Intrinsic Reaction Coordinate Scans

55. Input for IRC Calculation
StepSize=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 synonym for RCFC.

56. IRC Calculation in GaussView

57. Reaction Pathway Graph

58. Thermochemistry from ab initio Calculations

59. Thermochemistry from ab initio Calculations

60. Thermochemistry from frequency calculation

61. Modeling System in Solution

62. Calculating Solvent Effect

63. Calculating Solvent Effect

64. Solvent Effect: Menshutkin Model Reaction Transition State

65. Solvent Effect: Menshutkin Model Reaction Transition State

66. NMR Shielding Tensors

67. NMR Example Input %chk=ethynenmr #p hf/6-311+g(2d,p) nmr nmr ethyne
0 1 C
C,1,r1
H,1,r2,2,a2
H,2,r3,1,a3,3,d3,0
Variables
R1=
R2=
R3=
A2=180.0
A3=180.0
D3=0.0

70. Comparison of Calculated and Experimental Chemical Shifts

71. QM/MM: ONIOM Model

72. QM/MM: ONIOM Model From GaussView menu: Edit -> Select Layer
Low Layer
Medium Layer
High Layer

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

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

75. QM/MM: ONIOM Setup

76. What Is NBO? C-C Bond C-H Bond
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.
C-C Bond
C-H Bond

77. NBO Analysis

78. NBO in GaussView

79. Natural Population Analysis
#rhf/3-21g pop=nbo RHF/3-21G for formamide (H2NCHO)   H                 H                N                C                 O                 H               

80. NPA Output Sample

81. Gaussian & GaussView
Further Readings
11/13/2008
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 Gaussian
Research Computing Center, ITS

82. 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

83. Hands-on: Part II Calculate/View Molecular Orbitals with GaussView
Gaussian & GaussView
Hands-on: Part II
11/13/2008
Calculate/View Molecular Orbitals with GaussView
Calculate/View Electrostatic Potential with GaussView
Calculate/View Vibrational Frequencies in GaussView
Calculate/View NMR Tensors with GaussView
Calculate/View a Reaction Path with GaussView
Research Computing Center, ITS

84. Gaussian & GaussView
11/13/2008
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