Introduction to Gaussian
and GaussView
Shubin Liu, Ph.D.
Renaissance Computing Institute
University of North Carolina at Chapel Hill
Agenda
•
•
•
•
•
•
•
11/6/2006
Introduction
Capabilities
Input File Preparation
Gaussian GUI – GaussView
Run G03 Jobs @ UNC-CH
Some Advanced Topics
Hands-on Experiments
Introduction to Gaussian
2
Course Goal
•
•
•
•
•
•
11/6/2006
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
3
Pre-requisites
• Basic UNIX knowledge
• Introduction to Scientific Computing
• An account on Emerald
11/6/2006
Introduction to Gaussian
4
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
11/6/2006
Introduction to Gaussian
5
About You
• Name, department, group, interest?
• Any experience before with Gaussian or
GaussView?
• What do you expect to use them? What
kind of systems?
11/6/2006
Introduction to Gaussian
6
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: http://www.gaussian.com
11/6/2006
Introduction to Gaussian
7
Gaussian
11/6/2006
Introduction to Gaussian
8
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
11/6/2006
Introduction to Gaussian
9
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
11/6/2006
Introduction to Gaussian
10
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
11/6/2006
Introduction to Gaussian
11
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
11/6/2006
Introduction to Gaussian
12
Input File – Example 1
# HF/6-31G(d)
water energy
0 1
O -0.464 0.177 0.0
Coordinate
H -0.464 1.137 0.0
H 0.441 -0.143 0.0
!Route section
!Blank line
!Title section
!Blank line
!Charge & multiplicity
!Geometry in Cartesian
!Blank line
11/6/2006
Introduction to Gaussian
13
Input File – Example 2
%nproc=2
%chk=water.chk
#b3lyp/6-311+G(3df,2p) opt freq
Calcn Title: test
0 1
O
h 1 r
h 1 r 2 a
variables
r=0.98
a=109.
!Link 0 section
!Route/Keywords
!Blank line
!Title
!Ban line
!Charge & multiplicity
!Geometry in Z-matrix
!Blank line
11/6/2006
Introduction to Gaussian
14
Input File – Link 0 Commands
•
11/6/2006
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
15
Input File – Keyword Specification
•
•
•
•
•
•
11/6/2006
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
Introduction to Gaussian
16
11/6/2006
Introduction to Gaussian
17
Basis Set
•
•
•
•
•
•
11/6/2006
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
18
11/6/2006
Introduction to Gaussian
19
Input File – Title Specification
• Brief description of calculation –
for users benefit
• Terminate with a blank line
11/6/2006
Introduction to Gaussian
20
Input File – Molecular Geometry
•
•
•
•
11/6/2006
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
21
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
11/6/2006
Introduction to Gaussian
22
Other Gaussian Utilities
•
•
•
•
11/6/2006
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
23
GaussView
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: http://www.gaussian.com/g_gv/gvtop.htm
11/6/2006
Introduction to Gaussian
24
GaussView Availability
•
11/6/2006
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
25
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.
11/6/2006
Introduction to Gaussian
26
GaussView: Build
11/6/2006
Introduction to Gaussian
27
GaussView: Build
11/6/2006
Introduction to Gaussian
28
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 popup 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.
11/6/2006
Introduction to Gaussian
29
GaussView: Setup
11/6/2006
Introduction to Gaussian
30
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.
11/6/2006
Introduction to Gaussian
31
GuassView: Showing Results
11/6/2006
Introduction to Gaussian
32
Surfaces
11/6/2006
Introduction to Gaussian
33
Reflection-Absorption Infrared Spectrum of AlQ3
N
O
Al
O
N
N
O
Wavenumbers (cm-1)
752
11/6/2006
1000
1386
1338
1116
800
1473
1200
Introduction to Gaussian
1580 1605
1400
1600
34
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).
11/6/2006
Introduction to Gaussian
35
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).
11/6/2006
Introduction to Gaussian
36
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, emerald.isis.unc.edu
– LINUX Cluster, topsail.unc.edu (available upon request)
• Package information available at:
http://help.unc.edu/6082
11/6/2006
Introduction to Gaussian
37
Access GaussView
• From UNIX workstation
– Type “xhost + emerald.isis.unc.edu” or “xhost +
happy.isis.unc.edu”
– 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:
http://www.unc.edu/atn/hpc/applications/science/gaussian/access_gv/g03_gv_instructions.htm
11/6/2006
Introduction to Gaussian
38
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
11/6/2006
Introduction to Gaussian
39
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)
11/6/2006
Introduction to Gaussian
40
Default Settings
• Temporary files
– Yatta/cypress:
– Emerald:
• Memory
– Yatta/cypress:
– Emerald:
• MAXDISK
– Yatta/cypress:
– Emerald:
11/6/2006
/scr/APPS_SCRDIR
/tmp
1GB
512MB
4GB
2GB
Introduction to Gaussian
41
Advanced Topics
•
•
•
•
•
•
•
•
•
•
11/6/2006
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
42
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
11/6/2006
Introduction to Gaussian
43
Model Potential Energy Surface
11/6/2006
Introduction to Gaussian
44
Calculating PES in
Gaussian/GaussView
• Use the keyword “scan”
• Then change
input file properly
11/6/2006
Introduction to Gaussian
45
Transition State Search
11/6/2006
Introduction to Gaussian
46
Calculating Transition States
11/6/2006
Introduction to Gaussian
47
Locating Transition States
11/6/2006
Introduction to Gaussian
48
TS Search in Gaussian
11/6/2006
Introduction to Gaussian
49
TS Search in
Gaussian/GaussView
11/6/2006
Introduction to Gaussian
50
11/6/2006
Introduction to Gaussian
51
Animation of Imaginary Frequency
• Check that the imaginary
frequency corresponds to
the TS you search for.
11/6/2006
Introduction to Gaussian
52
Intrinsic Reaction Coordinate Scans
11/6/2006
Introduction to Gaussian
53
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.
11/6/2006
Introduction to Gaussian
54
IRC Calculation in GaussView
11/6/2006
Introduction to Gaussian
55
Reaction Pathway Graph
11/6/2006
Introduction to Gaussian
56
Thermochemistry
from ab initio Calculations
11/6/2006
Introduction to Gaussian
57
Thermochemistry
from ab initio Calculations
11/6/2006
Introduction to Gaussian
58
Thermochemistry from frequency
calculation
11/6/2006
Introduction to Gaussian
59
Modeling System in Solution
11/6/2006
Introduction to Gaussian
60
Calculating Solvent Effect
11/6/2006
Introduction to Gaussian
61
Calculating Solvent Effect
11/6/2006
Introduction to Gaussian
62
Solvent Effect: Menshutkin Model
Reaction Transition State
11/6/2006
Introduction to Gaussian
63
11/6/2006
Introduction to Gaussian
64
NMR Shielding Tensors
11/6/2006
Introduction to Gaussian
65
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
11/6/2006
Introduction to Gaussian
66
11/6/2006
Introduction to Gaussian
67
11/6/2006
Introduction to Gaussian
68
Comparison of Calculated and Experimental
Chemical Shifts
11/6/2006
Introduction to Gaussian
69
QM/MM: ONIOM Model
11/6/2006
Introduction to Gaussian
70
QM/MM: ONIOM Model
From GaussView menu: Edit -> Select Layer
Low Layer
11/6/2006
Medium Layer
Introduction to Gaussian
High Layer
71
QM/MM: ONIOM Setup
From GaussView menu: Calculate ->Gaussian->Method
11/6/2006
Introduction to Gaussian
72
QM/MM: ONIOM Setup
• For the medium and low layers:
11/6/2006
Introduction to Gaussian
73
QM/MM: ONIOM Setup
11/6/2006
Introduction to Gaussian
74
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
11/6/2006
C-H Bond
Introduction to Gaussian
75
NBO Analysis
11/6/2006
Introduction to Gaussian
76
NBO in GaussView
11/6/2006
Introduction to Gaussian
77
Natural Population Analysis
#rhf/3-21g pop=nbo
RHF/3-21G for formamide (H2NCHO)
0 1
H
H
N
C
O
H
11/6/2006
-1.908544
-1.188060
-1.084526
0.163001
1.196265
0.140159
0.420906
-1.161135
-0.157315
0.386691
-0.246372
1.492269
Introduction to Gaussian
0.000111
0.000063
0.000032
-0.000154
0.000051
0.000126
78
NPA
Output
Sample
11/6/2006
Introduction to Gaussian
79
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.)
11/6/2006
Introduction to Gaussian
80
QUESTIONS & COMMENTS?
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
11/6/2006
Introduction to Gaussian
81
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
11/6/2006
Introduction to Gaussian
82
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
11/6/2006
Introduction to Gaussian
83