Quantum Mechanics Calculations III

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Oct 29, 2013 (3 years and 9 months ago)

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Quantum Mechanics
Calculations III

Apr 2010

Postgrad

course on Comp
Chem

Noel M.
O’Boyle

Overview of QM methods

Including correlation


HF (“
ab

initio”)


Semi
-
empirical

Forcefields

DFT

Speed/Accuracy

Molecular
mechanics

Quantum
mechanics

(wavefunction)

Quantum
mechanics

(electron density)

Carrying out calculations


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

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


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

Input for a calculation


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


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
-
molecule
-
and.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
-
sn2
-
reaction.html


Finding the path connecting reactant to product (intrinsic reaction coordinate)


http://molecularmodelingbasics.blogspot.com/2009/10/get
-
reaction
-
intrinsic
-
reaction.html

Practical tips


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)