Transcript Gaussian 09 Tutorial

Gaussian 09 Tutorial
July 17, 2014 @ SCENT HPC Summer School @ GIST
Eunhwan Jung
Ph. D. Candidate
Molecular Modeling Laboratory (MML)
School of Materials Science and Engineering (MSE)
Gwangju Institute of Science and Technology (GIST)
1
Course contents
• General information of Gaussian 09
• Part 1: Preparing Input Files
- from Protein Data Bank (PDB)
- Build a Structure using GaussView
• Part 2: Running Gaussian 09 on tusmp
• Part 3: Visualization with GaussView
• Part 4: Practice
2
General information of Gaussian 09
• Gaussian website
www.gaussian.com
• Capability in Gaussian 09
 Energy, Geometry optimization
 DFT, TDDFT
 Solvation models
 Molecular properties
 NMR, UV-vis, IRC, partial charges
 Dipole moment, molecular orbitals
 Electrostatic potential charge, Mulliken population
PuTTY – SSH remote access client program
putty
http://the.earth.li/~sgtatham/putty/latest/x86/putty.exe
Xming download & install
xming
http://sourceforge.net/projects/xming/files/latest/download
Connect to PLSI system
• Connect to login node using SSH protocol
• User : remote access is permitted only described IP address on
application form with 22 port.
or
•
Use SSH utility such as Putty or SSH Secure Shell Client.
Connect to PLSI system
22
login01.plsi.or.kr
PLSI
Connect to PLSI system
• for X11 forwarding
Preparing input files
• Running files
 name.com : Gaussian input describing the desired calculation
 name.sh : executable script
 name.log : output file
 fort.7 : molecular orbital file
• Scratch files
 name.chk : check point file
 name.rwk : read-write file
 name.int : two electron integral file
 name.d2e : two electron integral derivative file
Preparing input files
• .com file in Gaussian 09
 %chk = : path of the check point file
 %mem = : specifying resource requirements
 %nproc= : number of CPU
Preparing input files
• .com file in Gaussian 09
 Calculation method
 Functional / basis set
 Calculation option
sp : single point energy
opt : geometry optimization
freq : frequency
irc : intrinsic reaction coordinate
pop : population
td : time dependent dft
scrf : self consistent reaction field
Preparing input files
• Title
• Charge, spin multiplicity
•
Molecule coordinate
Preparing input files (PDB)
benzene.pdb
pdb2xyz
http://www.rcsb.org/pdb/home/home.do
Preparing input files (GaussView)
Preparing input files
•
•
•
•
•
User email
Number of CPU, Memory
Calculation cluster
Job time
Job file name
Running Gaussian 09 on PLSI supercomputer
• Login node > calculation node
 ssh tusmp
• Keywords
 llstatus
 llq
#system status
#job status
Running Gaussian 09 on PLSI supercomputer
• Login node > calculation node
 exit
• Keywords
 llstatus
 llsubmit g09.sh
 llq
#system status
#submit the job
#job status
 llcancel job_id
#cancel the job
Visualization with GaussView
Visualization with GaussView
Visualization with GaussView
Practice
1. Geometry optimization
2. Molecular orbital
3. Time dependent DFT method
4. UV-vis spectrum
Q&A
• Torsion energy curves
• Absorption spectra
• Electronic structure
• Charge distribution & dipole moment
• Molecular orbital
LUMO
HOMO
• Binding energy
FFY
FFXS
FFXS
Binding Energy
(kcal/mol)
CF
24
FF
25
FF
23
FFX
FFY
22
FFYS
21
FFX
20
FFZ
FFYS
19
18
CF
FFZ
17
1 (BT)
4 (TPD)
Practice files
• Optimization
Practice files
• Optimization
Practice files
• Optimization