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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) G wangju Institute of Science and Technology ( G IST ). Course contents.

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Gaussian 09 Tutorial

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  1. 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) GwangjuInstitute of Science and Technology (GIST)

  2. Course contents • General information of Gaussian 09 • Part 1: Preparing InputFiles - 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 www.gaussian.com

  4. PuTTY – SSH remote access client program putty http://the.earth.li/~sgtatham/putty/latest/x86/putty.exe

  5. Xming download & install xming http://sourceforge.net/projects/xming/files/latest/download

  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 22 login01.plsi.or.kr PLSI

  8. Connect to PLSI system • for X11 forwarding

  9. 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

  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 http://www.rcsb.org/pdb/home/home.do

  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 • sshtusmp • 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 • llcanceljob_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. 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

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