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Gaussian & GaussView. Shubin Liu, Ph.D. Research Computing Center, ITS University of North Carolina at Chapel Hill. Agenda. Introduction Capabilities Input File Preparation Gaussian GUI – GaussView Run G03/G09 Jobs @ UNC-CH Some Advanced Topics Hands-on Experiments – next hour.
Gaussian & GaussView

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Slide 1

Gaussian & GaussView

Shubin Liu, Ph.D.

Research Computing Center, ITS

University of North Carolina at Chapel Hill

Slide 2

Agenda

  • Introduction

  • Capabilities

  • Input File Preparation

  • Gaussian GUI – GaussView

  • Run G03/G09 Jobs @ UNC-CH

  • Some Advanced Topics

  • Hands-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_html/divisions/rc/training/scientific/short_courses/

Slide 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

Slide 4

Pre-requisites

  • Basic UNIX knowledge

  • Introduction to Scientific Computing

  • An account on Emerald

Slide 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 SecurityIT Infrastructure and Operations

Research Computing CenterTeaching and Learning

User Support and EngagementOffice of the CIO

Communication TechnologiesCommunications

Enterprise ApplicationsFinance and Administration

Slide 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

Slide 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

Slide 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?

Slide 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

Slide 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

Slide 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

Slide 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)

Slide 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

Slide 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

Slide 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

Slide 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

  • Slide 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

    Slide 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

    Slide 23

    Input File – Title Specification

    • Brief description of calculation – for users benefit

    • Terminate with a blank line

    Slide 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

  • Slide 25

    A More Complicated Example

    %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--

    %chk=/scr/APPS_SCRDIR/f33em5p77c.chk

    %mem=4096MB

    %NProc=2

    # 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

    Slide 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)

    Slide 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

    Slide 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)

    Slide 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.

    Slide 30

    GaussView: Build

    Slide 31

    GaussView: Build

    Slide 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.

    Slide 33

    GaussView: Setup

    Slide 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.

    Slide 35

    GuassView: Showing Results

    Slide 36

    Surfaces

    Slide 37

    Reflection-Absorption Infrared Spectrum of AlQ3

    Wavenumbers (cm-1)

    1473

    752

    1386

    1338

    1116

    1580

    1605

    800

    1000

    1200

    1400

    1600

    Slide 38

    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).

    Slide 39

    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).

    Slide 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

    Slide 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

    Slide 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

    Slide 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

    Slide 44

    Default Settings

    • Temporary files

      • Emerald: /largefs/gausswork

    • Memory

      • Emerald: 512MB

    • MAXDISK

      • Emerald: 2GB

    Slide 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.

    Slide 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

    Slide 47

    Model Potential Energy Surface

    Slide 48

    Calculating PES in Gaussian/GaussView

    • Use the keyword “scan”

    • Then change

      input file properly

    Slide 49

    Transition State Search

    Slide 50

    Calculating Transition States

    Slide 51

    Locating Transition States

    Slide 52

    TS Search in Gaussian

    Slide 53

    TS Search inGaussian/GaussView

    Slide 54

    TS Search inGaussian/GaussView

    Slide 55

    Animation of Imaginary Frequency

    • Check that the imaginary

      frequency corresponds to

      the TS you search for.

    Slide 56

    Intrinsic Reaction Coordinate Scans

    Slide 57

    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.

    Slide 58

    IRC Calculation in GaussView

    Slide 59

    Reaction Pathway Graph

    Slide 60

    Thermochemistryfrom ab initio Calculations

    Slide 61

    Thermochemistryfrom ab initio Calculations

    Slide 62

    Thermochemistry from frequency calculation

    Slide 63

    Modeling System in Solution

    Slide 64

    Calculating Solvent Effect

    Slide 65

    Calculating Solvent Effect

    Slide 66

    Solvent Effect: Menshutkin Model Reaction Transition State

    Slide 67

    Solvent Effect: Menshutkin Model Reaction Transition State

    Slide 68

    NMR Shielding Tensors

    Slide 69

    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=1.20756258

    R2=1.06759666

    R3=1.06759666

    A2=180.0

    A3=180.0

    D3=0.0

    Slide 72

    Comparison of Calculated and Experimental Chemical Shifts

    Slide 73

    QM/MM: ONIOM Model

    Slide 74

    QM/MM: ONIOM Model

    From GaussView menu: Edit -> Select Layer

    Low Layer

    Medium Layer

    High Layer

    Slide 75

    QM/MM: ONIOM Setup

    From GaussView menu: Calculate->Gaussian->Method

    Slide 76

    QM/MM: ONIOM Setup

    • For the medium and low layers:

    Slide 77

    QM/MM: ONIOM Setup

    Slide 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.

    C-C Bond

    C-H Bond

    Slide 79

    NBO Analysis

    Slide 80

    NBO in GaussView

    Slide 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

    Slide 82

    NPA Output Sample

    Slide 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.)

    Slide 84

    Comments & Questions???

    Please direct comments/questions about Gaussian/GaussView to

    E-mail: research@unc.edu

    Please direct comments/questions pertaining to this presentation to

    E-Mail: shubin@email.unc.edu

    Slide 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

    The WORD .doc format of this hands-on exercises is available here:

    http://its2.unc.edu/divisions/rc/training/scientific/

    /afs/isis/depts/its/public_html/divisions/rc/training/scientific/short_courses/labDirections_gaussian_2009.doc

    Slide 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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