Professional Documents
Culture Documents
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/
its.unc.edu 2
Course Goal
its.unc.edu 3
Pre-requisites
its.unc.edu 4
About Us
its.unc.edu 5
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
its.unc.edu 6
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
its.unc.edu 7
About You
its.unc.edu 8
Gaussian & GaussView
its.unc.edu 9
its.unc.edu 10
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
its.unc.edu 11
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
its.unc.edu 12
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)
its.unc.edu 13
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
its.unc.edu 14
Input File – Example 1
its.unc.edu 15
Input File – Example 2
its.unc.edu 16
Input File – Link 0 Commands
its.unc.edu 17
Input File – Keyword Specification
its.unc.edu 18
its.unc.edu 19
its.unc.edu 20
Basis Set
its.unc.edu 21
its.unc.edu 22
Input File – Title Specification
its.unc.edu 23
Input File – Molecular Geometry
its.unc.edu 24
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
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
its.unc.edu 25
Other Gaussian Utilities
its.unc.edu 26
GaussView
its.unc.edu 27
GaussView Availability
Support platforms:
– IBM RS6000 (AIX 5.1) (Happy/yatta/p575)
– LINUX 32-bit OS (Emeraldtest)
– LINUX 64-bit OS (Emerald, Topsail, Kure)
its.unc.edu 28
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.
its.unc.edu 29
GaussView: Build
its.unc.edu 30
GaussView: Build
its.unc.edu 31
GuassView: Setup
its.unc.edu 33
GuassView: Showing Results
its.unc.edu 34
GuassView: Showing Results
its.unc.edu 35
Surfaces
its.unc.edu 36
Reflection-Absorption Infrared Spectrum of AlQ3
N O
O Al N
N O
its.unc.edu 37
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).
its.unc.edu 38
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).
its.unc.edu 39
Gaussian/GaussView @ UNC
its.unc.edu 40
Access GaussView
ssh -X emerlad.isis.unc.edu
its.unc.edu 41
Submit G03 Jobs to Servers
For example:
bsub -q idle -R blade g03 input.inp
its.unc.edu 42
Submit G03 Jobs to Servers
To submit multiple-CPU G03 jobs via LSF:
-- G03 is parallelized via OpenMP
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)
its.unc.edu 43
Default Settings
Temporary files
• Emerald: /largefs/gausswork
Memory
• Emerald: 512MB
MAXDISK
• Emerald: 2GB
its.unc.edu 44
Advanced Topics
its.unc.edu 45
Potential Energy
Surfaces
its.unc.edu 46
Model Potential Energy Surface
its.unc.edu 47
Calculating PES in
Gaussian/GaussView
Then change
input file properly
its.unc.edu 48
Transition State Search
its.unc.edu 49
Calculating Transition
States
its.unc.edu 50
Locating Transition
States
its.unc.edu 51
TS Search in Gaussian
its.unc.edu 52
TS Search in
Gaussian/GaussView
its.unc.edu 53
TS Search in
Gaussian/GaussView
its.unc.edu 54
Animation of Imaginary
Frequency
its.unc.edu 55
Intrinsic Reaction Coordinate Scans
its.unc.edu 56
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.
its.unc.edu 57
IRC Calculation in
GaussView
its.unc.edu 58
Reaction Pathway Graph
its.unc.edu 59
Thermochemistry
from ab initio Calculations
its.unc.edu 60
Thermochemistry
from ab initio Calculations
its.unc.edu 61
Thermochemistry from frequency
calculation
its.unc.edu 62
Modeling System in Solution
its.unc.edu 63
Calculating Solvent Effect
its.unc.edu 64
Calculating Solvent Effect
its.unc.edu 65
Solvent Effect: Menshutkin Model
Reaction Transition State
its.unc.edu 66
Solvent Effect: Menshutkin Model
Reaction Transition State
its.unc.edu 67
NMR Shielding Tensors
its.unc.edu 68
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
its.unc.edu 69
its.unc.edu 70
its.unc.edu 71
Comparison of Calculated and
Experimental Chemical Shifts
its.unc.edu 72
QM/MM: ONIOM Model
its.unc.edu 73
QM/MM: ONIOM Model
its.unc.edu 74
QM/MM: ONIOM Setup
its.unc.edu 75
QM/MM: ONIOM Setup
its.unc.edu 76
QM/MM: ONIOM Setup
its.unc.edu 77
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.
its.unc.edu 78
NBO Analysis
its.unc.edu 79
NBO in GaussView
its.unc.edu 80
Natural Population Analysis
#rhf/3-21g pop=nbo
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
its.unc.edu 81
NPA
Output
Sample
its.unc.edu 82
Further Readings
its.unc.edu 83
Comments & Questions???
its.unc.edu 86