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Introduction to Gaussian and GaussView. Shubin Liu, Ph.D. Renaissance Computing Institute University of North Carolina at Chapel Hill. Agenda. Introduction Capabilities Input File Preparation Gaussian GUI – GaussView Run G03 Jobs @ UNC-CH Some Advanced Topics Hands-on Experiments.

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Introduction to gaussian and gaussview

Introduction to Gaussian and GaussView

Shubin Liu, Ph.D.

Renaissance Computing Institute

University of North Carolina at Chapel Hill


  • Introduction

  • Capabilities

  • Input File Preparation

  • Gaussian GUI – GaussView

  • Run G03 Jobs @ UNC-CH

  • Some Advanced Topics

  • Hands-on Experiments

Introduction to Gaussian

Course goal
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

Introduction to Gaussian

Pre requisites

  • Basic UNIX knowledge

  • Introduction to Scientific Computing

  • An account on Emerald

Introduction to Gaussian

About myself
About Myself

  • Ph.D. from Chemistry, UNC-CH

  • Currently Senior Computational Scientist @ UNC ITS Research Computing Division

  • Responsibilities:

    • Support Comp Chem/Phys/Material Science software, Support Programming (FORTRAN/C/C++) tools, code porting, parallel computing, etc.

    • Engagement projects with faculty members on campus

    • Conduct own research on Comp Chem

      • DFT theory and concept

      • Systems in biological and material science

Introduction to Gaussian

About you
About You

  • Name, department, group, interest?

  • Any experience before with Gaussian or GaussView?

  • What do you expect to use them? What kind of systems?

Introduction to Gaussian

Gaussian gaussview
Gaussian & GaussView

  • Gaussian 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 make calculation preparation and output analysis easier, quicker and more efficient. Current version 3.0.9.

  • Vendor’s website:

Introduction to Gaussian


Introduction to Gaussian

Gaussian 98 03 functionality
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

Introduction to Gaussian

Gaussian 98 03 functionality1
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

Introduction to Gaussian

New in gaussian 03
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

Introduction to Gaussian

Gaussian input file structure
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

Introduction to Gaussian

Input file example 1
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

Introduction to Gaussian

Input file example 2
Input File – Example 2

%nproc=2 !Link 0 section


#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




!Blank line

Introduction to Gaussian

Input file link 0 commands
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

  • Introduction to Gaussian

    Input file keyword specification
    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

    Introduction to Gaussian

    Basis set
    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

    Introduction to Gaussian

    Input file title specification
    Input File – Title Specification

    • Brief description of calculation – for users benefit

    • Terminate with a blank line

    Introduction to Gaussian

    Input file molecular geometry
    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

  • Introduction to Gaussian

    A more complicated example
    A More Complicated Example




    #B3LYP/6-31G* opt geom=Checkpoint Guess=read nosymm scf=tight

    Geometry optimization of a sample molecule

    1 1





    # B3LYP/6-311++G** sp pop=nbo nosymm guess=read geom=checkpoint

    Single Point Energy for the "reference state" of molecule with one more electron.

    0 2

    Introduction to Gaussian

    Other gaussian utilities
    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)

    Introduction to Gaussian


    GaussView 3.0.9 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:

    Introduction to Gaussian

    Gaussview availability
    GaussView Availability

    • Support platforms:

      – IBM RS6000 (AIX 5.1)

      – SGI (IRIX 6.5.3)

      – Intel Pentium II, III, IV/Athlon (IA32) Linux

      (RedHat 8.0, 9.0; SuSE 8.2, 9.0, 9.1)

    Introduction to Gaussian

    Gaussview build
    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.

    Introduction to Gaussian

    Gaussview build1
    GaussView: Build

    Introduction to Gaussian

    Gaussview build2
    GaussView: Build

    Introduction to Gaussian

    Guassview setup
    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.

    Introduction to Gaussian

    Gaussview setup
    GaussView: Setup

    Introduction to Gaussian

    Guassview showing results
    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.

    Introduction to Gaussian

    Guassview showing results1
    GuassView: Showing Results

    Introduction to Gaussian


    Introduction to Gaussian

    Reflection absorption infrared spectrum of alq3
    Reflection-Absorption Infrared Spectrum of AlQ3

    Wavenumbers (cm-1)













    Introduction to Gaussian

    Gaussview vcd vibrational circular dichroism spectra
    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).

    Introduction to Gaussian

    Gaussview oniom
    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).

    Introduction to Gaussian

    Gaussian gaussview @ unc
    Gaussian/GaussView @ UNC

    • Installed in AFS ISIS package space /afs/isis/pkg/gaussian

      • Package name: gaussian

      • Versions: 03C02, 03D02 (default version)

      • Type “ipm add gaussian” to subscribe the service

    • Availability

      • SGI Altix 3700, cedar/cypress

      • IBM P690, happy/yatta

      • LINUX cluster,

      • LINUX Cluster, (available upon request)

    • Package information available at:

    Introduction to Gaussian

    Access gaussview
    Access GaussView

    • From UNIX workstation

      • Type “xhost +” or “xhost +”

      • Login to emerald 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:

    Introduction to Gaussian

    Submit g03 jobs to servers
    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 yatta g03 input.inp

      bsub -q idle -R blade g03 input.inp

    Introduction to Gaussian

    Submit g03 jobs to servers1
    Submit G03 Jobs to Servers

    • To submit multiple-CPU G03 jobs via LSF:

      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., “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

      On Emerald, only serial G03 is available because G03 is parallelized via OpenMP (for share-memory SMP machines)

    Introduction to Gaussian

    Default settings
    Default Settings

    • Temporary files

      • Yatta/cypress: /scr/APPS_SCRDIR

      • Emerald: /tmp

    • Memory

      • Yatta/cypress: 1GB

      • Emerald: 512MB


      • Yatta/cypress: 4GB

      • Emerald: 2GB

    Introduction to Gaussian

    Advanced topics
    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.

    Introduction to Gaussian

    Potential energy surfaces
    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

    Introduction to Gaussian

    Model potential energy surface
    Model Potential Energy Surface

    Introduction to Gaussian

    Calculating pes in gaussian gaussview
    Calculating PES in Gaussian/GaussView

    • Use the keyword “scan”

    • Then change

      input file properly

    Introduction to Gaussian

    Transition state search
    Transition State Search

    Introduction to Gaussian

    Calculating transition states
    Calculating Transition States

    Introduction to Gaussian

    Locating transition states
    Locating Transition States

    Introduction to Gaussian

    Ts search in gaussian
    TS Search in Gaussian

    Introduction to Gaussian

    Ts search in gaussian gaussview
    TS Search inGaussian/GaussView

    Introduction to Gaussian

    Animation of imaginary frequency
    Animation of Imaginary Frequency

    • Check that the imaginary

      frequency corresponds to

      the TS you search for.

    Introduction to Gaussian

    Intrinsic reaction coordinate scans
    Intrinsic Reaction Coordinate Scans

    Introduction to Gaussian

    Input for irc calculation
    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.

    Introduction to Gaussian

    Irc calculation in gaussview
    IRC Calculation in GaussView

    Introduction to Gaussian

    Reaction pathway graph
    Reaction Pathway Graph

    Introduction to Gaussian

    Thermochemistry from ab initio calculations
    Thermochemistryfrom ab initio Calculations

    Introduction to Gaussian

    Thermochemistry from ab initio calculations1
    Thermochemistryfrom ab initio Calculations

    Introduction to Gaussian

    Modeling system in solution
    Modeling System in Solution

    Introduction to Gaussian

    Calculating solvent effect
    Calculating Solvent Effect

    Introduction to Gaussian

    Calculating solvent effect1
    Calculating Solvent Effect

    Introduction to Gaussian

    Nmr shielding tensors
    NMR Shielding Tensors

    Introduction to Gaussian

    Nmr example input
    NMR Example Input


    #p hf/6-311+g(2d,p) nmr

    nmr ethyne

    0 1












    Introduction to Gaussian

    Qm mm oniom model
    QM/MM: ONIOM Model

    Introduction to Gaussian

    Qm mm oniom model1
    QM/MM: ONIOM Model

    From GaussView menu: Edit -> Select Layer

    Low Layer

    Medium Layer

    High Layer

    Introduction to Gaussian

    Qm mm oniom setup
    QM/MM: ONIOM Setup

    From GaussView menu: Calculate->Gaussian->Method

    Introduction to Gaussian

    Qm mm oniom setup1
    QM/MM: ONIOM Setup

    • For the medium and low layers:

    Introduction to Gaussian

    Qm mm oniom setup2
    QM/MM: ONIOM Setup

    Introduction to Gaussian

    What is nbo
    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.

    C-C Bond

    C-H Bond

    Introduction to Gaussian

    Nbo analysis
    NBO Analysis

    Introduction to Gaussian

    Nbo in gaussview
    NBO in GaussView

    Introduction to Gaussian

    Natural population analysis
    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

    Introduction to Gaussian

    NPA Output Sample

    Introduction to Gaussian

    Further readings
    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.)

    Introduction to Gaussian


    Please direct comments/questions about Gaussian/GaussView to

    E-mail: [email protected]

    Please direct comments/questions pertaining to this presentation to

    E-Mail: [email protected]

    Introduction to Gaussian

    Hands on part i
    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,

    • 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

    Introduction to Gaussian

    Hands on part ii
    Hands-on: Part II

    • 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


    Introduction to Gaussian