Noel M. O’Boyle
Apr 2010
Postgrad course on Comp Chem

Molecular mechanics
Quantum mechanics
(wavefunction)
Including correlation
HF (“ab initio”)
Quantum mechanics
(electron density)
DFT
Semi-empirical
Forcefields

• http://en.wikipedia.org/wiki/List_of_quantum_chemistry_and_solid_state_physics_soft ware
• Gaussian (commercial)
– 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)
• ORCA (free for academics)
– 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)
– Semi-empirical calculations, Stewart
•
NWChem (free for academics)
– General purpose
– http://www.emsl.pnl.gov/capabilities/computing/nwchem/
• GAMESS (available for free)
– General purpose calculations. (See next page)
• Firefly
– Fork of GAMESS, formerly “PC GAMESS”
– Faster than GAMESS (especially on Windows)
•
PSI3 (Open Source)
– HF and higher level
– http://www.psicode.org/, no Windows support

– Avogadro (OS, http://avogadro.sf.net)
– GaussView (commercial, available when buying Gaussian)
– 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

• GAMESS is free (but not open-source) software developed by the Gordon Group and collaborators
• To get it...
– 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
• To install it...
– Run the installer
– Click Next a few times
– It installs to C:\WinGAMESS
•
To use it...
– Documentation is in C:\WinGAMESS\manuals
– Following C:\WinGAMESS\manuals\WinGAMESS.pdf we can...
• 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?
– Install Avogadro and MacMolPlt

• 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

• http://molecularmodelingbasics.blogspot.com/
• Look at all of Jan’s screencasts and posts starting from the oldest
– On the right-hand side, see under Blog Archive
• Tools of the trade (all free, some open source)
– http://molecularmodelingbasics.blogspot.com/2009/06/tools-of-trade.html
•
Building a molecule
– http://molecularmodelingbasics.blogspot.com/2009/07/building-complicated-molecule-2d-to-
3d.html
• Finding the lowest energy conformer
– http://molecularmodelingbasics.blogspot.com/2009/07/building-complicated-moleculeand.html
• Look at the GAMESS input file
– http://molecularmodelingbasics.blogspot.com/2009/07/some-gamess-input-basics_24.html
• Set up a calculation using Avogadro
– http://molecularmodelingbasics.blogspot.com/2009/07/typical-set-of-gamess-calculations.html
• Finding a transition state
– http://molecularmodelingbasics.blogspot.com/2009/08/finding-transition-state-sn2reaction.html
• Finding the path connecting reactant to product (intrinsic reaction coordinate)
– http://molecularmodelingbasics.blogspot.com/2009/10/get-reaction-intrinsic-reaction.html

• 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)