Overview of QM methods

Report
Quantum Mechanics
Calculations III
Noel M. O’Boyle
Apr 2010
Postgrad course on Comp Chem
Overview of QM methods
Molecular
mechanics
Quantum
mechanics
(wavefunction)
Quantum
mechanics
(electron density)
Including correlation
Speed/Accuracy
HF (“ab initio”)
Semi-empirical
Forcefields
DFT
Carrying out calculations
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http://en.wikipedia.org/wiki/List_of_quantum_chemistry_and_solid_state_physics_soft
ware
Gaussian (commercial)
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ORCA (free for academics)
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General purpose calculations. (See next page)
Firefly
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General purpose
http://www.emsl.pnl.gov/capabilities/computing/nwchem/
GAMESS (available for free)
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Semi-empirical calculations, Stewart
NWChem (free for academics)
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General purpose
http://www.thch.uni-bonn.de/tc/orca/
Lots of other commercial packages: ADF (for DFT), Jaguar
MOPAC2009 (commercial but free for academics)
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The most widely used package
Can do most everything, and is pretty robust. Presumably not the fastest (the only software
whose license prohibits published comparisons).
Gaussian09 available through ICHEC, also faster (8-CPU machines)
Fork of GAMESS, formerly “PC GAMESS”
Faster than GAMESS (especially on Windows)
PSI3 (Open Source)
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HF and higher level
http://www.psicode.org/, no Windows support
Once you have the QM software...
• Set up calculations
– Avogadro (OS, http://avogadro.sf.net)
– GaussView (commercial, available when
buying Gaussian)
• Analyse results
– Avogadro
– Molekel (OS, http://molekel.cscs.ch)
– GaussSum (OS, http://gausssum.sf.net, by
me)
– MacMolPlt (free,
http://www.scl.ameslab.gov/MacMolPlt/)
– ...and many others
Get GAMESS
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GAMESS is free (but not open-source) software developed by the Gordon Group and
collaborators
To get it...
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To install it...
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Go to http://www.msg.ameslab.gov/GAMESS/
Click on “How to get GAMESS”
Click “Obtaining GAMESS”
Click “I agree”
Enter email address, and tick box for “GAMESS version January 12, 2009 R3 for Microsoft
Windows” (also a ChemOffice version – haven’t tried it)
Click “Submit request”
You will receive an email with a link, and a username and password
Follow the link to download the installer and enter the username and password when
requested
Run the installer
Click Next a few times
It installs to C:\WinGAMESS
To use it...
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Documentation is in C:\WinGAMESS\manuals
Following C:\WinGAMESS\manuals\WinGAMESS.pdf we can...
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Create a shortcut to C:\WinGAMESS\WG_DDE.bat on the desktop
Drag-and-drop GAMESS input files onto this shortcut
How do we create an input file?
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Install Avogadro and MacMolPlt
Input for a calculation
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What type of calculation to do
Location and atomic number of atoms
Charge on molecule
Multiplicity of molecule
• No need for bond orders
• No need to say where the charge is
– The charge is simply used to calculate the total
number of electrons
• Typical calculations are in vacuo
– i.e. not in solid or liquid state, or in solvent
– If required, there is software for handling bulk solids,
and there are methods to include solvent effects
Jan Jensen’s GAMESS Screencasts
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http://molecularmodelingbasics.blogspot.com/
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Look at all of Jan’s screencasts and posts starting from the oldest
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Tools of the trade (all free, some open source)
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http://molecularmodelingbasics.blogspot.com/2009/07/typical-set-of-gamess-calculations.html
Finding a transition state
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http://molecularmodelingbasics.blogspot.com/2009/07/some-gamess-input-basics_24.html
Set up a calculation using Avogadro
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http://molecularmodelingbasics.blogspot.com/2009/07/building-complicated-moleculeand.html
Look at the GAMESS input file
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http://molecularmodelingbasics.blogspot.com/2009/07/building-complicated-molecule-2d-to3d.html
Finding the lowest energy conformer
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http://molecularmodelingbasics.blogspot.com/2009/06/tools-of-trade.html
Building a molecule
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On the right-hand side, see under Blog Archive
http://molecularmodelingbasics.blogspot.com/2009/08/finding-transition-state-sn2reaction.html
Finding the path connecting reactant to product (intrinsic reaction coordinate)
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http://molecularmodelingbasics.blogspot.com/2009/10/get-reaction-intrinsic-reaction.html
Practical tips
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To speed up a geometry optimization, you can optimise first with a
smaller basis set and then continue from there
If you have trouble with SCF convergence, it can be a good idea to try
converging it with a smaller basis set first and then projecting from that
as the initial guess
Molecules with geometrical symmetry will be corresponding faster (on
the other hand, if you require symmetry to be broken during the
calculation, you should turn off symmetry perception)

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