1. Gaussian 09 Tutorial Ph. D. Candidate
July 17, SCENT HPC Summer GIST
Eunhwan Jung
Ph. D. Candidate
Molecular Modeling Laboratory (MML)
School of Materials Science and Engineering (MSE)
Gwangju Institute of Science and Technology (GIST)

2. 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

3. 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

4. PuTTY – SSH remote access client program

5. Xming download & install

6. 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.

7. Connect to PLSI system
login01.plsi.or.kr 22
PLSI

8. Connect to PLSI system
for X11 forwarding

9. Preparing input files Running files Scratch 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

10. Preparing input files .com file in Gaussian 09
%chk = : path of the check point file
%mem = : specifying resource requirements
%nproc= : number of CPU

11. 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

12. Preparing input files Title Charge, spin multiplicity
Molecule coordinate

13. Preparing input files (PDB)
benzene.pdb
pdb2xyz

14. Preparing input files (GaussView)

15. Preparing input files User email Number of CPU, Memory
Calculation cluster
Job time
Job file name

16. Running Gaussian 09 on PLSI supercomputer
Login node > calculation node
ssh tusmp
Keywords
llstatus #system status
llq #job status

17. 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

18. Visualization with GaussView

19. Visualization with GaussView

20. Visualization with GaussView

21. Practice Geometry optimization Molecular orbital
Time dependent DFT method
UV-vis spectrum

22. Q & A

23. Charge distribution & dipole moment Molecular orbital
Torsion energy curves
Absorption spectra
Electronic structure
Charge distribution & dipole moment
Molecular orbital
LUMO
HOMO

24. Binding energy

25. Practice files
Optimization

26. Practice files
Optimization

27. Practice files
Optimization