Gaussian 09 Tutorial
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Transcript of Gaussian 09 Tutorial
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Gaussian 09 Tutorial
Eunhwan Jung
Ph. D. CandidateMolecular Modeling Laboratory (MML)
School of Materials Science and Engineering (MSE)Gwangju Institute of Science and Technology (GIST)
July 17, 2014 @ SCENT HPC Summer School @ GIST
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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
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General information of Gaussian 09
• Gaussian website
• 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
www.gaussian.com
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PuTTY – SSH remote access client program
putty
http://the.earth.li/~sgtatham/putty/latest/x86/put-ty.exe
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Xming download & install
xming
http://sourceforge.net/projects/xming/files/latest/down-load
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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.
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login01.plsi.or.kr
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PLSI
Connect to PLSI system
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Connect to PLSI system
• for X11 forwarding
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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
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Preparing input files • .com file in Gaussian 09
%chk = : path of the check point file %mem = : specifying resource requirements %nproc= : number of CPU
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Preparing input files • .com file in Gaussian 09
Calculation method Functional / basis set
Calculation option
sp : single point energyopt : geometry optimizationfreq : frequencyirc : intrinsic reaction coordinatepop : populationtd : time dependent dftscrf : self consistent reaction field
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Preparing input files • Title• Charge, spin multiplicity• Molecule coordinate
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Preparing input files (PDB)
http://www.rcsb.org/pdb/home/home.do
pdb2xyz
benzene.pdb
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Preparing input files (GaussView)
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Preparing input files
• User email• Number of CPU, Memory• Calculation cluster• Job time• Job file name
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Running Gaussian 09 on PLSI supercomputer
• Login node > calculation node ssh tusmp
• Keywords llstatus #system status llq #job status
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Running Gaussian 09 on PLSI supercomputer
• Login node > calculation node exit
• Keywords llstatus #system status llsubmit g09.sh #submit the job llq #job status
llcancel job_id #cancel the job
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Visualization with GaussView
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Visualization with GaussView
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Visualization with GaussView
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Practice
1. Geometry optimization
2. Molecular orbital
3. Time dependent DFT method
4. UV-vis spectrum
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Q & A
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• Torsion energy curves
• Absorption spectra
• Electronic structure
• Charge distribution & dipole moment • Molecular orbital
LUMO
HOMO
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Binding Energy(kcal/mol)
25
21
19
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22
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18
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FFXS
FFY
FFX
FF
FFYS
4 (TPD)1 (BT)
CF
FFZ
CF
FFXS
FFY
FF
FFX
FFZ
FFYS
• Binding energy
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Practice files
• Optimization
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Practice files
• Optimization
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Practice files
• Optimization