View
80
Download
3
Category
Tags:
Preview:
DESCRIPTION
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) G wangju Institute of Science and Technology ( G IST ). Course contents. - PowerPoint PPT Presentation
Citation preview
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
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
• 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
PuTTY – SSH remote access client program
putty
http://the.earth.li/~sgtatham/putty/latest/x86/put-ty.exe
Xming download & install
xming
http://sourceforge.net/projects/xming/files/latest/down-load
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.
login01.plsi.or.kr
22
PLSI
Connect to PLSI system
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 energyopt : geometry optimizationfreq : frequencyirc : intrinsic reaction coordinatepop : populationtd : time dependent dftscrf : self consistent reaction field
Preparing input files • Title• Charge, spin multiplicity• Molecule coordinate
Preparing input files (PDB)
http://www.rcsb.org/pdb/home/home.do
pdb2xyz
benzene.pdb
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 #system status llq #job status
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
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(kcal/mol)
25
21
19
23
24
22
20
18
17
FFXS
FFY
FFX
FF
FFYS
4 (TPD)1 (BT)
CF
FFZ
CF
FFXS
FFY
FF
FFX
FFZ
FFYS
• Binding energy
Practice files
• Optimization
Practice files
• Optimization
Practice files
• Optimization
Recommended