Introduction to Gaussian & GaussView Shubin Liu, Ph.D. Research Computing Center, ITS University of North Carolina at Chapel Hill

Introduction to Introduction to Gaussian & GaussViewGaussian & GaussView

Introduction to Introduction to Gaussian & GaussViewGaussian & GaussView

Shubin Liu, Ph.D.Research Computing Center, ITS

University of North Carolina at Chapel Hill

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AgendaAgenda

Introduction

Capabilities

Input File Preparation

Gaussian GUI – GaussView

Run G03 Jobs @ UNC-CH

Some Advanced Topics

Hands-on Experiments – next hour

The PDF format of this presentation is available here:http://www.unc.edu/~shubin/Courses/Gaussian_GaussView.pdf

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Course GoalCourse 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

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Pre-requisitesPre-requisites

Basic UNIX knowledge

Introduction to Scientific Computing

An account on Emerald

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About Us

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

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Research Computing Center

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

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About MyselfAbout 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

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Gaussian & GaussViewGaussian & 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 4.1.2.

Vendor’s website: http://www.gaussian.com

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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

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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

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New in Gaussian 03New 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

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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

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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

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%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

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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

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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

http://www.gaussian.com/g_ur/keywords.htm

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Basis SetBasis 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

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Input File – Title Specification

Input File – Title Specification

Brief description of calculation – for users benefit

Terminate with a blank line

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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

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A More Complicated Example

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

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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)

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GaussView 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

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GaussView Availability 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)

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GaussView: BuildGaussView: 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.

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GuassView: SetupGuassView: 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.

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GaussView: SetupGaussView: Setup

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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.

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SurfacesSurfaces

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Reflection-Absorption Infrared Spectrum of AlQ3Reflection-Absorption Infrared Spectrum of AlQ3

ON

AlO

ON

N

752

1116 1338

13861473

1580 1605

160014001200800 1000

Wavenumbers (cm-1)

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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).

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GaussView: ONIOMGaussView: 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).

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Gaussian/GaussView @ UNC

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:

http://help.unc.edu/6082

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Access GaussViewAccess 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:http://www.unc.edu/atn/hpc/applications/science/gaussian/access_gv/g03_gv_instructions.htm

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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.inpbsub -q month -m p575-n02 g03 input.inpbsub -q idle -R blade g03 input.inp

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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

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Default SettingsDefault Settings

Temporary files

• P575/Yatta/cypress: /scr/APPS_SCRDIR

• Emerald: /tmp

Memory

• P575/Yatta/cypress: 1GB

• Emerald: 512MB

MAXDISK

• P575/Yatta/cypress: 4GB

• Emerald: 2GB

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Advanced TopicsAdvanced 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.

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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

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Model Potential Energy Surface

Model Potential Energy Surface

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Calculating PES in Gaussian/GaussView

Calculating PES in Gaussian/GaussView

Use the keyword “scan”

Then change

input file properly

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Transition State SearchTransition State Search

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Calculating Transition States

Calculating Transition States

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Locating Transition States

Locating Transition States

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TS Search in Gaussian

TS Search in Gaussian

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TS Search inGaussian/GaussView


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Animation of Imaginary Frequency

Animation of Imaginary Frequency

Check that the imaginary

frequency corresponds to

the TS you search for.

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Intrinsic Reaction Coordinate Scans

Intrinsic Reaction Coordinate Scans

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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.

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IRC Calculation in GaussView

IRC Calculation in GaussView

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Reaction Pathway Graph

Reaction Pathway Graph

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Thermochemistryfrom ab initio

Calculations


Calculations

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Calculations


Calculations

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Thermochemistry from frequency calculation

Thermochemistry from frequency calculation

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Modeling System in Solution

Modeling System in Solution

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Calculating Solvent Effect


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Solvent Effect: Menshutkin Model Reaction Transition

State


State

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State


State

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NMR Shielding TensorsNMR Shielding Tensors

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NMR Example InputNMR Example Input

%chk=ethynenmr#p hf/6-311+g(2d,p) nmr

nmr ethyne

0 1CC,1,r1H,1,r2,2,a2H,2,r3,1,a3,3,d3,0 VariablesR1=1.20756258R2=1.06759666R3=1.06759666A2=180.0A3=180.0D3=0.0

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Comparison of Calculated and Experimental Chemical ShiftsComparison of Calculated and Experimental Chemical Shifts

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QM/MM: ONIOM Model

QM/MM: ONIOM Model

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QM/MM: ONIOM Model

QM/MM: ONIOM Model

From GaussView menu: Edit -> Select Layer

Low Layer Medium Layer High Layer

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QM/MM: ONIOM Setup

QM/MM: ONIOM Setup

From GaussView menu: Calculate ->Gaussian->Method

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QM/MM: ONIOM Setup

QM/MM: ONIOM Setup

For the medium and low layers:

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QM/MM: ONIOM Setup

QM/MM: ONIOM Setup

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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 BondC-C Bond C-H BondC-H Bond

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NBO AnalysisNBO Analysis

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NBO in GaussViewNBO in GaussView

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Natural Population AnalysisNatural 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

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NPA Output

Sample

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Further ReadingsFurther 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.)

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Hands-on: Part IHands-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

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Hands-on: Part IIHands-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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Comments & Questions???Comments & Questions???

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]

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]

Documents

Introduction to Gaussian & GaussView Shubin Liu, Ph.D. Research Computing Center, ITS University of North Carolina at Chapel Hill