Gaussian 09 Tutorial Ph. D. Candidate 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)

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

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 http://the.earth.li/~sgtatham/putty/latest/x86/putty.exe

Xming download & install 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 login01.plsi.or.kr 22 PLSI

Connect to PLSI system for X11 forwarding

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

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 #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 Geometry optimization Molecular orbital Time dependent DFT method UV-vis spectrum

Q & A

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

Binding energy

Practice files Optimization

Practice files Optimization

Practice files Optimization