introducontoiqmol:partiiopenshell.usc.edu/chem545/lectures2014/iqmol-intro-i.pdf · iqmol youtube...
TRANSCRIPT
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Introduc)on to IQmol: Part I !!!
Shirin Faraji, Ilya Kaliman, and Anna Krylov
!
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Resources
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Written by Dr. Andrew Gilbert !
Keep yourself up to date with IQmol website: http://iqmol.org !
IQmol Youtube channel: IQmol now has its own Youtube channel
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Building molecules
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Open IQmol, the molecule building screen looks like this:
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Main build tools
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Build Mode
Build Elements (periodic table)
Add Hydrogens
Add Fragments (pre-build molecules)
Minimize Energy (classical forcefield)
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Building molecules
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Click the “Build Element” : periodic table pops-up:
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Selec)ng atom
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Select an atom, for example Oxygen: O Click in the blue screen area to place the Oxygen atom
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Add Hydrogen
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Click the “Add Hydrogens” button:
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Classical minimizer
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Click the “Minimize Energy” button to get a more realistic structure
Energy of the current structure
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Build —> Select Force Field : allows you to choose different force field
Classical minimizer
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Pre-‐build molecules
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Pre-build molecule library (“Add Fragments” button) contains various molecules that can be used to build more complex molecules
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Click on the “Add Fragment” button , then choose amino_acids/L-lysine.
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Pre-‐build molecules
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Click the “Add Fragment” button again, choosing the same molecule. Hold CTRL and the right mouse button (two fingers on Mac Trackpad) and drag the highlighted molecule – the screen should now look like this:
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Pre-‐build molecules
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Manipula)on Mode
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Click on the “Manipulate” mode !
Use left mouse button to rotate Use right mouse button to translate
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Select Mode
Click on the “Select” mode !
Click on atoms to select them Click anywhere on the main window to deselect atoms Press “Alt” and the right mouse (two fingers on Mac Trackpad) button to move the group
of selected atoms
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Measuring bond length, angles, and dihedrals
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Click the select bu6on
Select 2, 3 or 4 atoms as necessary
the measured bond length, angle or dihedral is displayed in the bo6om corner:
The bond angle is displayed here
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Performing Q-‐Chem calcula)ons Example 1: H2O
!
!
Prerequisite: Consult IQmol-Server-Setup tutorial
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!• Build molecule, clean-up (force-field opt-n), check symmetry (symmetrize molecule) • Optimize B3LYP/6-31G* • Play with changing the view of the molecule, move it around, zoom • Use ‘Select’ feature to measure bonds and angles • Look at MOs: HOMO, HOMO-1; LUMO • Run FREQ job, look at vibrations (click versus double-click)
H2O
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Building up/Check symmetry
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Performing Q-‐Chem
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! Calculation —> Q-chem Setup; Open Q-chem User Interface (QUI) input editor
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QUI
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QUI has 2 windows
Details of the calculation Preview of the input file
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QUI
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There are 2 windows in “Computational details” section
Basic setup
Advanced calculations
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SePng up the job type, method, basis set
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SePng up the job type, method, basis set
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SePng up the job type, method, basis set
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H2O: Op)miza)on and Frequency
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Take H2O molecule and perform “Optimization” and “Frequency” analysis First optimization:
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Use add button to submit multiple jobs within on input file: such and optimization and frequency to be performed subsequently
Read the geometry from the previous calculation
New job starts
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H2O: Op)miza)on and Frequency
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Input edi)ng
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One can manually modify the input preview !!
$rem section
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Saving input file
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Save the input on a disk: File —> save as Use .inp for name of the input file !
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Give a name and remember it.
SubmiPng job to HPC
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- Use default queue on HPCC; - Leave the rest of settings unchanged. !For advanced users: - To run Q-Chem in parallel (openmp), change the number in CPUs (consult the manual to see which types of jobs are openmp-parallelized); - for MPI-parallel, you will need to tweak the settings in the previous page; - Memory and scratch settings are not impor tan t he re , bu t fo r op t ima l performance you may need to tweak these settings in the Q-Chem input file, especially for advanced calculations. Consult the manual before doing so!
Choosing queue
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Job Status
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Check the job status by selecting: “Calculation —>Job Monitor”
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Check the job status by selecting: “Calculation —>Job Monitor”
Monitoring submiVed job
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Job status is displayed in a new window:
use leD mouse bu6on to select the job
use right mouse bu6on to see this menu
kill the job by selecFng this opFon
Monitoring submiVed job
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Job is finished
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Note: Must be the same name as the folder you have created while submiPng the job
Copy files to your laptop
If they do not match, you will get “no valid data found in …” error message. The files are actually OK and are copied to you laptop. You can open them individually with “Open…” command.
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AYer you copied files to your laptop
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Golden star shows that it is copied properly !Click the checkbox !
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Analyzing Output: Op)miza)on
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After the calculations has completed, open the .out (output) with iQmol. The example here is H2O after optimization and frequency analysis.
Click the small arrow next to the checkbox to see various calculated properties
Clicking the arrow next to Geometr ies g ives the calculated energy at every step of opFmizaFon
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Analyzing Output: Frequencies
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Clicking the arrow next to Frequencies gives the calculated frequencies and displaced vectors for each frequency (for H2O: 3N-6=3 vibrational frequencies)
Double click at each value to animate the vibration
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Analyzing Output: Orbitals, Density, Spin Density ,…
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Must add GUI = 2 in the $ rem section (IQmol does it by default) Open .Fchk file to see orbitals, density, spin density and so on. Click at Surfaces and a window pops-up
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Select orbital Select the relevant orbital (default: HOMO) Select the quality you want Click calculate !!!!
click the arrow next to Surfaces to see the orbitals one by one by clicking the checkbox of the corresponding orbital (do not forget to uncheck the old one)
Use “Manipulation” mode to better see the orbital ! To save the screen: File —> Save Picture
Analyzing Output: Orbitals, Density, Spin Density ,…
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Select different properties to be calculated; spin density, density, and so on….
Analyzing Output: Orbitals, Density, Spin Density ,…
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Performing Q-‐Chem calcula)ons Example 2: CH2O (Formaldehyde)
!
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Formaldehyde
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!• Build molecule, clean-up (force-field opt-n), check symmetry (symmetrize molecule) • Optimize wB97X-D/6-31+G* • Play with changing the view of the molecule, move it around, zoom • Use ‘Select’ feature to measure bonds and angles • Look at MOs: HOMO, HOMO-1, LUMO • Run FREQ job, look at vibrations (click versus double-click) • Advanced: Run NBO analysis, look at NBO charges and bond orders
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Building up/Check symmetry
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CH2O Op)miza)on
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CH2O Frequency
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SubmiPng job to HPC
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Choosing queue
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Monitoring submiVed job
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Monitoring submiVed job
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Job is finished
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Copy files to your laptop
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Analyze the output
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click checkbox
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Op)miza)on cycles
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Frequencies
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3N-‐6= 6 vibraFonal frequency
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Measuring parameters
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Use “Select” mode to choose a bond, angle, torsion, …
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HOMO-‐LOMO orbitals
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Must add GUI = 2 in the $ rem section (IQmol does it by default) Open .Fchk file to see Orbitals, Density, Spin density and so on. Click at Surfaces and a window will pops-up
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Select Orbital Select the relevant orbital (default: HOMO) Select the quality you want Click calculate !!!
Click the arrow next to Surfaces to see the orbitals one by one by clicking the checkbox of the corresponding orbital (do not forget to uncheck the old one)
Use Manipulation Mode to better see the orbital ! To save the screen: File —> Save Picture
HOMO-‐LOMO orbitals