Agenda
Introduction
Capabilities
Input File Preparation
Gaussian GUI GaussView
Run G03/G09 Jobs @ UNC-CH
Some Advanced Topics
http://its2.unc.edu/divisions/rc/training/scientific/
/afs/isis/depts/its/public_html/divisions/rc/training/scientific/short_courses/
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Course Goal
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Pre-requisites
Basic UNIX knowledge
Introduction to Scientific Computing
An account on Emerald
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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
Research Computing Center
User Support and Engagement
Communication Technologies
Enterprise Applications
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Communications
Finance and Administration
Research Computing
Center
Where and who are we and what do we do?
Groups
Infrastructure -- Hardware
User Support -- Software
Engagement -- Collaboration
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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
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About You
Name, department, group, interest?
Any experience before with Gaussian or
GaussView?
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Populations analyses
Electrostatic potentials
NMR tensors
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BOMD Born-Oppenheimer MD
ADMP Atom-Centered Density Matrix Propagation
Periodic Boundary Conditions (PBC) HF and DFT energies and
gradients
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# HF/6-31G(d)
!Route section
!Blank line
water energy
!Title section
!Blank line
0 1
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!Link 0 section
!Route/Keywords
!Blank line
!Title
!Ban line
!Charge & multiplicity
!Geometry in Z-matrix
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%chk
%chk=myjob.chk
%mem=12MW
%mem
%nproc
$nproc=4
%rwf=1,1999mb,b,1999mb
%sc=e,1999mb,f,1999mb
%rwf
%scr
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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
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Cartesian coordinate
Label x y z
Z-matrix
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--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
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GaussView
GaussView 4.1.2 makes using Gaussian 03 simple and straightforward:
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Set up and submit Gaussian 03 jobs right from the interface, and
monitor their progress as they run.
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GaussView Availability
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Support platforms:
IBM RS6000 (AIX 5.1) (Happy/yatta/p575)
LINUX 32-bit OS (Emeraldtest)
LINUX 64-bit OS (Emerald, Topsail, Kure)
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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.
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GaussView: Build
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GaussView: Build
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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 Builders 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.
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GaussView: Setup
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Surfaces
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O
Al
O
N
N
O
Wavenumbers (cm-1)
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1000
1386
1338
1116
800
1473
1200
1580 1605
1400
1600
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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. sterle, K. B. Wiberg, J. R. Cheeseman, and M. J. Frisch, J. Org. Chem. 67, 8090 (2002).
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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).
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Gaussian/GaussView @ UNC
Installed in AFS ISIS package space /afs/isis/pkg/gaussian
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Access GaussView
From UNIX workstation
Login to emerald, kure, topsail
ssh -X emerlad.isis.unc.edu
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-m mname
g03 input.inp
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-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 Settings
Temporary files
Emerald:
/largefs/gausswork
Memory
Emerald:
512MB
MAXDISK
Emerald:
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2GB
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Advanced Topics
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Potential Energy
Surfaces
Many aspects of chemistry can be reduced to questions about
potential energy surfaces (PES)
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Calculating PES in
Gaussian/GaussView
Use the keyword scan
Then change
input file properly
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Calculating Transition
States
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Locating Transition
States
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TS Search in Gaussian
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TS Search in
Gaussian/GaussView
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TS Search in
Gaussian/GaussView
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Animation of Imaginary
Frequency
Check that the imaginary
frequency corresponds to
the TS you search for.
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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
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Thermochemistry
from ab initio Calculations
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Thermochemistry
from ab initio Calculations
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%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
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Low Layer
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Medium Layer
High Layer
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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
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C-H Bond
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NBO Analysis
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NBO in GaussView
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#rhf/3-21g pop=nbo
RHF/3-21G for formamide (H2NCHO)
0 1
H
H
N
C
O
H
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-1.908544
-1.188060
-1.084526
0.163001
1.196265
0.140159
0.420906
-1.161135
-0.157315
0.386691
-0.246372
1.492269
0.000111
0.000063
0.000032
-0.000154
0.000051
0.000126
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NPA
Output
Sample
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Further Readings
Computational Chemistry (Oxford Chemistry Primer) G. H. Grant and
W. G. Richards (Oxford University Press)
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Hands-on: Part I
http://its2.unc.edu/divisions/rc/training/scientific/
/afs/isis/depts/its/public_html/divisions/rc/training/scientific/short_courses/labDirections_gaussian_2009.doc
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Hands-on: Part II
Calculate/View Molecular Orbitals with GaussView
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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.ht
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