gaussian 09 tutorial

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