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University College Cork Lecture Series on Computational Chemistry - Lecture 3

University College Cork Lecture Series on Computational Chemistry - Lecture 3

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- 1. Quantum Mechanics Calculations III<br />Noel M. O’Boyle<br />Apr 2010<br />Postgrad course on Comp Chem<br />
- 2. Overview of QM methods<br />Molecular mechanics<br />Quantum mechanics<br />(wavefunction)<br />Quantum mechanics<br />(electron density)<br />Including correlation<br />HF (“ab initio”)<br />Semi-empirical<br />DFT<br />Speed/Accuracy<br />Forcefields<br />
- 3. Carrying out calculations<br />http://en.wikipedia.org/wiki/List_of_quantum_chemistry_and_solid_state_physics_software<br />Gaussian (commercial)<br />The most widely used package<br />Can do most everything, and is pretty robust. Presumably not the fastest (the only software whose license prohibits published comparisons).<br />Gaussian09 available through ICHEC, also faster (8-CPU machines)<br />ORCA (free for academics)<br />General purpose<br />http://www.thch.uni-bonn.de/tc/orca/<br />Lots of other commercial packages: ADF (for DFT), Jaguar<br />MOPAC2009 (commercial but free for academics)<br />Semi-empirical calculations, Stewart<br />NWChem (free for academics)<br />General purpose<br />http://www.emsl.pnl.gov/capabilities/computing/nwchem/<br />GAMESS (available for free)<br />General purpose calculations. (See next page)<br />Firefly<br />Fork of GAMESS, formerly “PC GAMESS”<br />Faster than GAMESS (especially on Windows)<br />PSI3 (Open Source)<br />HF and higher level<br />http://www.psicode.org/, no Windows support<br />
- 4. Once you have the QM software...<br />Set up calculations<br />Avogadro (OS, http://avogadro.sf.net)<br />GaussView (commercial, available when buying Gaussian)<br />Analyse results<br />Avogadro<br />Molekel (OS, http://molekel.cscs.ch)<br />GaussSum (OS, http://gausssum.sf.net, by me)<br />MacMolPlt (free, http://www.scl.ameslab.gov/MacMolPlt/)<br />...and many others<br />
- 5. Get GAMESS<br />GAMESS is free (but not open-source) software developed by the Gordon Group and collaborators<br />To get it...<br />Go to http://www.msg.ameslab.gov/GAMESS/<br />Click on “How to get GAMESS”<br />Click “Obtaining GAMESS”<br />Click “I agree”<br />Enter email address, and tick box for “GAMESS version January 12, 2009 R3 for Microsoft Windows” (also a ChemOffice version – haven’t tried it)<br />Click “Submit request”<br />You will receive an email with a link, and a username and password<br />Follow the link to download the installer and enter the username and password when requested<br />To install it...<br />Run the installer<br />Click Next a few times<br />It installs to C:WinGAMESS<br />To use it...<br />Documentation is in C:WinGAMESSmanuals<br />Following C:WinGAMESSmanualsWinGAMESS.pdf we can...<br />Create a shortcut to C:WinGAMESSWG_DDE.bat on the desktop<br />Drag-and-drop GAMESS input files onto this shortcut<br />How do we create an input file?<br />Install Avogadro and MacMolPlt<br />
- 6. Input for a calculation<br />What type of calculation to do<br />Location and atomic number of atoms<br />Charge on molecule<br />Multiplicity of molecule<br />No need for bond orders<br />No need to say where the charge is<br />The charge is simply used to calculate the total number of electrons<br />Typical calculations are in vacuo<br />i.e. not in solid or liquid state, or in solvent<br />If required, there is software for handling bulk solids, and there are methods to include solvent effects<br />
- 7. Jan Jensen’s GAMESS Screencasts<br />http://molecularmodelingbasics.blogspot.com/<br />Look at all of Jan’s screencasts and posts starting from the oldest<br />On the right-hand side, see under Blog Archive<br />Tools of the trade (all free, some open source)<br />http://molecularmodelingbasics.blogspot.com/2009/06/tools-of-trade.html<br />Building a molecule<br />http://molecularmodelingbasics.blogspot.com/2009/07/building-complicated-molecule-2d-to-3d.html<br />Finding the lowest energy conformer<br />http://molecularmodelingbasics.blogspot.com/2009/07/building-complicated-molecule-and.html<br />Look at the GAMESS input file<br />http://molecularmodelingbasics.blogspot.com/2009/07/some-gamess-input-basics_24.html<br />Set up a calculation using Avogadro<br />http://molecularmodelingbasics.blogspot.com/2009/07/typical-set-of-gamess-calculations.html<br />Finding a transition state<br />http://molecularmodelingbasics.blogspot.com/2009/08/finding-transition-state-sn2-reaction.html<br />Finding the path connecting reactant to product (intrinsic reaction coordinate)<br />http://molecularmodelingbasics.blogspot.com/2009/10/get-reaction-intrinsic-reaction.html<br />
- 8. Practical tips<br />To speed up a geometry optimization, you can optimise first with a smaller basis set and then continue from there<br />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<br />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)<br />

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