Introduction to GAMESS calculations¶
Contents:
Install required software¶
The following instructions describe how to obtain and install GAMESS, Avogadro and wxMacMolPlt on Windows (as of April 2011).
Install GAMESS
Follow the “How to get GAMESS” link from the GAMESS website. When you finally get to the download page, enter your email address and tick the box for “GAMESS version October 1, 2010 R1 for Microsoft Windows”, and click Submit Request.
After a couple of minutes, you will receive an email containing a link to the WinGAMESS download along with a password. Click on the link and enter the password to download the installer. Run the installer and choose all of the defaults. In particular, you should make sure to install to
C:/WinGAMESS.You need to correct an error in
C:/WinGAMESS/WG_DDE.bat. Open theC:/WinGAMESSfolder, right-click onC:/WinGAMESS/WG_DDE.batand choose Edit. Change line 40 of the file to read as follows:set WinGamess_Version=10
Naturally, if you are using a different version of GAMESS, you should set this value appropriately.
- To test your GAMESS installation, save this GAMESS input file ethane.inp on your Desktop, open the folder
C:/WinGAMESS, and drag-and-dropethane.inpontoWG_DDE.bat. The first time you do this, you may have to say Yes twice to allow it through the Windows firewall (this requires Administrator rights). If GAMESS is working properly, it will create a fileethane.outon your Desktop.
Install Avogadro
Download Avogadro 1.0.1 from http://avogadro.openmolecules.net, using the Get Avogadro link. Run the installer.
Install wxMacMolPlt
wxMacmolPlot 7.4.2 is available from http://www.scl.ameslab.gov/MacMolPlt/. The download link is towards the bottom of the page. Run the installer.
Looking at GAMESS output¶
When you run GAMESS, an output file (or “log file”) is created. This is a text file that contains all of the results of the calculation.
Example output file¶
The following output file (available as a 6-page PDF here) is the result of a single point RHF/STO-3G calculation on a water molecule. A series of questions follows.
Distributed Data Interface kickoff program.
Initiating 2 compute processes on 2 nodes to run the following command:
C:\WinGAMESS/gamess.10.exe water_sym
******************************************************
* GAMESS VERSION = 1 OCT 2010 (R1) *
* FROM IOWA STATE UNIVERSITY *
* M.W.SCHMIDT, K.K.BALDRIDGE, J.A.BOATZ, S.T.ELBERT, *
* M.S.GORDON, J.H.JENSEN, S.KOSEKI, N.MATSUNAGA, *
* K.A.NGUYEN, S.J.SU, T.L.WINDUS, *
* TOGETHER WITH M.DUPUIS, J.A.MONTGOMERY *
* J.COMPUT.CHEM. 14, 1347-1363(1993) *
**************** 32 BIT LINUX VERSION ****************
SINCE 1993, STUDENTS AND POSTDOCS WORKING AT IOWA STATE UNIVERSITY
AND ALSO IN THEIR VARIOUS JOBS AFTER LEAVING ISU HAVE MADE IMPORTANT
CONTRIBUTIONS TO THE CODE:
IVANA ADAMOVIC, CHRISTINE AIKENS, YURI ALEXEEV, POOJA ARORA,
ANDREY ASADCHEV, ROB BELL, PRADIPTA BANDYOPADHYAY, JONATHAN BENTZ,
BRETT BODE, GALINA CHABAN, WEI CHEN, CHEOL HO CHOI, PAUL DAY, TIM DUDLEY,
DMITRI FEDOROV, GRAHAM FLETCHER, MARK FREITAG, KURT GLAESEMANN, DAN KEMP,
GRANT MERRILL, NORIYUKI MINEZAWA, JONATHAN MULLIN, TAKESHI NAGATA,
SEAN NEDD, HEATHER NETZLOFF, BOSILJKA NJEGIC, RYAN OLSON, MIKE PAK,
JIM SHOEMAKER, LYUDMILA SLIPCHENKO, SAROM SOK, JIE SONG,
TETSUYA TAKETSUGU, SIMON WEBB, SOOHAENG YOO, FEDERICO ZAHARIEV
ADDITIONAL CODE HAS BEEN PROVIDED BY COLLABORATORS IN OTHER GROUPS:
IOWA STATE UNIVERSITY:
JOE IVANIC, LAIMUTIS BYTAUTAS, KLAUS RUEDENBERG
UNIVERSITY OF TOKYO: KIMIHIKO HIRAO, TAKAHITO NAKAJIMA,
TAKAO TSUNEDA, MUNEAKI KAMIYA, SUSUMU YANAGISAWA,
KIYOSHI YAGI, MAHITO CHIBA, SEIKEN TOKURA, NAOAKI KAWAKAMI
UNIVERSITY OF AARHUS: FRANK JENSEN
UNIVERSITY OF IOWA: VISVALDAS KAIRYS, HUI LI
NATIONAL INST. OF STANDARDS AND TECHNOLOGY: WALT STEVENS, DAVID GARMER
UNIVERSITY OF PISA: BENEDETTA MENNUCCI, JACOPO TOMASI
UNIVERSITY OF MEMPHIS: HENRY KURTZ, PRAKASHAN KORAMBATH
UNIVERSITY OF ALBERTA: TOBY ZENG, MARIUSZ KLOBUKOWSKI
UNIVERSITY OF NEW ENGLAND: MARK SPACKMAN
MIE UNIVERSITY: HIROAKI UMEDA
MICHIGAN STATE UNIVERSITY:
KAROL KOWALSKI, MARTA WLOCH, JEFFREY GOUR, JESSE LUTZ, PIOTR PIECUCH
UNIVERSITY OF SILESIA: MONIKA MUSIAL, STANISLAW KUCHARSKI
FACULTES UNIVERSITAIRES NOTRE-DAME DE LA PAIX:
OLIVIER QUINET, BENOIT CHAMPAGNE
UNIVERSITY OF CALIFORNIA - SANTA BARBARA: BERNARD KIRTMAN
INSTITUTE FOR MOLECULAR SCIENCE:
KAZUYA ISHIMURA, MICHIO KATOUDA, AND SHIGERU NAGASE
UNIVERSITY OF NOTRE DAME: DAN CHIPMAN
KYUSHU UNIVERSITY:
HARUYUKI NAKANO,
FENG LONG GU, JACEK KORCHOWIEC, MARCIN MAKOWSKI, AND YURIKO AOKI,
HIROTOSHI MORI AND EISAKU MIYOSHI
PENNSYLVANIA STATE UNIVERSITY:
TZVETELIN IORDANOV, CHET SWALINA, JONATHAN SKONE,
SHARON HAMMES-SCHIFFER
WASEDA UNIVERSITY:
MASATO KOBAYASHI, TOMOKO AKAMA, HIROMI NAKAI
UNIVERSITY OF NEBRASKA:
PEIFENG SU, DEJUN SI, YALI WANG, HUI LI
UNIVERSITY OF ZURICH:
ROBERTO PEVERATI, KIM BALDRIDGE
N. COPERNICUS UNIVERSITY AND JACKSON STATE UNIVERSITY:
MARIA BARYSZ
PARALLEL VERSION RUNNING ON 2 PROCESSORS IN 2 NODES.
EXECUTION OF GAMESS BEGUN Mon Apr 11 13:58:57 2011
ECHO OF THE FIRST FEW INPUT CARDS -
INPUT CARD>! File created by MacMolPlt 7.4
INPUT CARD> $CONTRL SCFTYP=RHF RUNTYP=ENERGY MAXIT=30 MULT=1 $END
INPUT CARD> $SYSTEM TIMLIM=525600 MEMORY=1000000 $END
INPUT CARD> $BASIS GBASIS=STO NGAUSS=3 $END
INPUT CARD> $SCF DIRSCF=.TRUE. $END
INPUT CARD> $DATA
INPUT CARD>Title
INPUT CARD>CNV 2
INPUT CARD>
INPUT CARD>O 8.0 0.00000 0.00000 -0.06673
INPUT CARD>H 1.0 0.76334 0.00000 0.52965
INPUT CARD> $END
1000000 WORDS OF MEMORY AVAILABLE
BASIS OPTIONS
-------------
GBASIS=STO IGAUSS= 3 POLAR=NONE
NDFUNC= 0 NFFUNC= 0 DIFFSP= F
NPFUNC= 0 DIFFS= F BASNAM=
RUN TITLE
---------
Title
THE POINT GROUP OF THE MOLECULE IS CNV
THE ORDER OF THE PRINCIPAL AXIS IS 2
ATOM ATOMIC COORDINATES (BOHR)
CHARGE X Y Z
O 8.0 0.0000000000 0.0000000000 -0.1261014152
H 1.0 -1.4425034355 0.0000000000 1.0008933694
H 1.0 1.4425034355 0.0000000000 1.0008933694
INTERNUCLEAR DISTANCES (ANGS.)
------------------------------
1 O 2 H 3 H
1 O 0.0000000 0.9686883 * 0.9686883 *
2 H 0.9686883 * 0.0000000 1.5266800 *
3 H 0.9686883 * 1.5266800 * 0.0000000
* ... LESS THAN 3.000
ATOMIC BASIS SET
----------------
THE CONTRACTED PRIMITIVE FUNCTIONS HAVE BEEN UNNORMALIZED
THE CONTRACTED BASIS FUNCTIONS ARE NOW NORMALIZED TO UNITY
SHELL TYPE PRIMITIVE EXPONENT CONTRACTION COEFFICIENT(S)
O
1 S 1 130.7093214 0.154328967295
1 S 2 23.8088661 0.535328142282
1 S 3 6.4436083 0.444634542185
2 L 4 5.0331513 -0.099967229187 0.155916274999
2 L 5 1.1695961 0.399512826089 0.607683718598
2 L 6 0.3803890 0.700115468880 0.391957393099
H
4 S 7 3.4252509 0.154328967295
4 S 8 0.6239137 0.535328142282
4 S 9 0.1688554 0.444634542185
TOTAL NUMBER OF BASIS SET SHELLS = 4
NUMBER OF CARTESIAN GAUSSIAN BASIS FUNCTIONS = 7
NUMBER OF ELECTRONS = 10
CHARGE OF MOLECULE = 0
SPIN MULTIPLICITY = 1
NUMBER OF OCCUPIED ORBITALS (ALPHA) = 5
NUMBER OF OCCUPIED ORBITALS (BETA ) = 5
TOTAL NUMBER OF ATOMS = 3
THE NUCLEAR REPULSION ENERGY IS 9.0871358664
$CONTRL OPTIONS
---------------
SCFTYP=RHF RUNTYP=ENERGY EXETYP=RUN
MPLEVL= 0 CITYP =NONE CCTYP =NONE VBTYP =NONE
DFTTYP=NONE TDDFT =NONE
MULT = 1 ICHARG= 0 NZVAR = 0 COORD =UNIQUE
PP =NONE RELWFN=NONE LOCAL =NONE NUMGRD= F
ISPHER= -1 NOSYM = 0 MAXIT = 30 UNITS =ANGS
PLTORB= F MOLPLT= F AIMPAC= F FRIEND=
NPRINT= 7 IREST = 0 GEOM =INPUT
NORMF = 0 NORMP = 0 ITOL = 20 ICUT = 9
INTTYP=BEST GRDTYP=BEST QMTTOL= 1.0E-06
$SYSTEM OPTIONS
---------------
REPLICATED MEMORY= 1000000 WORDS (ON EVERY NODE).
DISTRIBUTED MEMDDI= 0 MILLION WORDS IN AGGREGATE,
MEMDDI DISTRIBUTED OVER 2 PROCESSORS IS 0 WORDS/PROCESSOR.
TOTAL MEMORY REQUESTED ON EACH PROCESSOR= 1000000 WORDS.
TIMLIM= 525600.00 MINUTES, OR 365.0 DAYS.
PARALL= T BALTYP= DLB KDIAG= 0 COREFL= F
MXSEQ2= 300 MXSEQ3= 150
----------------
PROPERTIES INPUT
----------------
MOMENTS FIELD POTENTIAL DENSITY
IEMOM = 1 IEFLD = 0 IEPOT = 0 IEDEN = 0
WHERE =COMASS WHERE =NUCLEI WHERE =NUCLEI WHERE =NUCLEI
OUTPUT=BOTH OUTPUT=BOTH OUTPUT=BOTH OUTPUT=BOTH
IEMINT= 0 IEFINT= 0 IEDINT= 0
MORB = 0
EXTRAPOLATION IN EFFECT
ORBITAL PRINTING OPTION: NPREO= 1 7 2 1
-------------------------------
INTEGRAL TRANSFORMATION OPTIONS
-------------------------------
NWORD = 0
CUTOFF = 1.0E-09 MPTRAN = 0
DIRTRF = T AOINTS =DUP
----------------------
INTEGRAL INPUT OPTIONS
----------------------
NOPK = 1 NORDER= 0 SCHWRZ= T
------------------------------------------
THE POINT GROUP IS CNV, NAXIS= 2, ORDER= 4
------------------------------------------
DIMENSIONS OF THE SYMMETRY SUBSPACES ARE
A1 = 4 A2 = 0 B1 = 2 B2 = 1
..... DONE SETTING UP THE RUN .....
CPU 0: STEP CPU TIME= 0.02 TOTAL CPU TIME= 0.0 ( 0.0 MIN)
TOTAL WALL CLOCK TIME= 0.0 SECONDS, CPU UTILIZATION IS 93.75%
********************
1 ELECTRON INTEGRALS
********************
...... END OF ONE-ELECTRON INTEGRALS ......
CPU 0: STEP CPU TIME= 0.00 TOTAL CPU TIME= 0.0 ( 0.0 MIN)
TOTAL WALL CLOCK TIME= 0.0 SECONDS, CPU UTILIZATION IS 93.75%
-------------
GUESS OPTIONS
-------------
GUESS =HUCKEL NORB = 0 NORDER= 0
MIX = F PRTMO = F PUNMO = F
TOLZ = 1.0E-08 TOLE = 1.0E-05
SYMDEN= F PURIFY= F
INITIAL GUESS ORBITALS GENERATED BY HUCKEL ROUTINE.
HUCKEL GUESS REQUIRES 2569 WORDS.
SYMMETRIES FOR INITIAL GUESS ORBITALS FOLLOW. BOTH SET(S).
5 ORBITALS ARE OCCUPIED ( 1 CORE ORBITALS).
2=A1 3=B1 4=A1 5=B2 6=B1 7=A1
...... END OF INITIAL ORBITAL SELECTION ......
CPU 0: STEP CPU TIME= 0.00 TOTAL CPU TIME= 0.0 ( 0.0 MIN)
TOTAL WALL CLOCK TIME= 0.0 SECONDS, CPU UTILIZATION IS 93.75%
----------------------
AO INTEGRAL TECHNOLOGY
----------------------
S,P,L SHELL ROTATED AXIS INTEGRALS, REPROGRAMMED BY
KAZUYA ISHIMURA (IMS) AND JOSE SIERRA (SYNSTAR).
S,P,D,L SHELL ROTATED AXIS INTEGRALS PROGRAMMED BY
KAZUYA ISHIMURA (INSTITUTE FOR MOLECULAR SCIENCE).
S,P,D,F,G SHELL TO TOTAL QUARTET ANGULAR MOMENTUM SUM 5,
ERIC PROGRAM BY GRAHAM FLETCHER (ELORET AND NASA ADVANCED
SUPERCOMPUTING DIVISION, AMES RESEARCH CENTER).
S,P,D,F,G,L SHELL GENERAL RYS QUADRATURE PROGRAMMED BY
MICHEL DUPUIS (PACIFIC NORTHWEST NATIONAL LABORATORY).
--------------------
2 ELECTRON INTEGRALS
--------------------
DIRECT SCF METHOD SKIPS INTEGRAL STORAGE ON DISK.
DIRECT TRANSFORMATION SKIPS AO INTEGRAL STORAGE ON DISK.
...... END OF TWO-ELECTRON INTEGRALS .....
CPU 0: STEP CPU TIME= 0.05 TOTAL CPU TIME= 0.1 ( 0.0 MIN)
TOTAL WALL CLOCK TIME= 0.1 SECONDS, CPU UTILIZATION IS 79.49%
--------------------------
RHF SCF CALCULATION
--------------------------
NUCLEAR ENERGY = 9.0871358664
MAXIT = 30 NPUNCH= 2
EXTRAP=T DAMP=F SHIFT=F RSTRCT=F DIIS=F DEM=F SOSCF=F
DENSITY MATRIX CONV= 2.00E-05
MEMORY REQUIRED FOR RHF ITERS= 44817 WORDS.
DIRECT SCF CALCULATION, SCHWRZ=T FDIFF=T, DIRTHR= 0.00E+00 NITDIR=10
SCHWARZ INEQUALITY OVERHEAD: 28 INTEGRALS, T= 0.00
NONZERO BLOCKS
ITER EX DEM TOTAL ENERGY E CHANGE DENSITY CHANGE DIIS ERROR INTEGRALS SKIPPED
1 0 0 -74.7974092796 -74.7974092796 0.596869468 0.000000000 141 0
2 1 0 -74.9507257506 -0.1533164709 0.181657794 0.000000000 141 0
3 2 0 -74.9629281338 -0.0122023833 0.059598419 0.000000000 141 0
4 3 0 -74.9642035242 -0.0012753904 0.020216252 0.000000000 141 0
5 4 0 -74.9643795359 -0.0001760117 0.007366384 0.000000000 141 0
6 0 0 -74.9644088533 -0.0000293174 0.004742101 0.000000000 141 0
7 1 0 -74.9644154231 -0.0000065699 0.000070104 0.000000000 141 0
8 2 0 -74.9644154252 -0.0000000021 0.000025327 0.000000000 141 0
9 3 0 -74.9644154256 -0.0000000003 0.000009752 0.000000000 141 0
-----------------
DENSITY CONVERGED
-----------------
TIME TO FORM FOCK OPERATORS= 0.0 SECONDS ( 0.0 SEC/ITER)
FOCK TIME ON FIRST ITERATION= 0.0, LAST ITERATION= 0.0
TIME TO SOLVE SCF EQUATIONS= 0.0 SECONDS ( 0.0 SEC/ITER)
FINAL RHF ENERGY IS -74.9644154256 AFTER 9 ITERATIONS
------------
EIGENVECTORS
------------
1 2 3 4 5
-20.2438 -1.2632 -0.6111 -0.4529 -0.3909
A1 A1 B1 A1 B2
1 O 1 S 0.994158 -0.233200 -0.000000 0.102889 0.000000
2 O 1 S 0.026315 0.837618 -0.000000 -0.534598 0.000000
3 O 1 X -0.000000 0.000000 0.606792 -0.000000 0.000000
4 O 1 Y -0.000000 0.000000 -0.000000 -0.000000 1.000000
5 O 1 Z 0.004251 0.126155 -0.000000 0.772609 0.000000
6 H 2 S -0.005841 0.157816 -0.446042 0.282964 0.000000
7 H 3 S -0.005841 0.157816 0.446042 0.282964 0.000000
6 7
0.5952 0.7274
A1 B1
1 O 1 S -0.130529 0.000000
2 O 1 S 0.863693 0.000000
3 O 1 X 0.000000 0.982566
4 O 1 Y 0.000000 0.000000
5 O 1 Z 0.744429 0.000000
6 H 2 S -0.788315 0.828700
7 H 3 S -0.788315 -0.828700
...... END OF RHF CALCULATION ......
CPU 0: STEP CPU TIME= 0.00 TOTAL CPU TIME= 0.1 ( 0.0 MIN)
TOTAL WALL CLOCK TIME= 0.1 SECONDS, CPU UTILIZATION IS 79.49%
----------------------------------------------------------------
PROPERTY VALUES FOR THE RHF SELF-CONSISTENT FIELD WAVEFUNCTION
----------------------------------------------------------------
-----------------
ENERGY COMPONENTS
-----------------
WAVEFUNCTION NORMALIZATION = 1.0000000000
ONE ELECTRON ENERGY = -122.1793235802
TWO ELECTRON ENERGY = 38.1277722882
NUCLEAR REPULSION ENERGY = 9.0871358664
------------------
TOTAL ENERGY = -74.9644154256
ELECTRON-ELECTRON POTENTIAL ENERGY = 38.1277722882
NUCLEUS-ELECTRON POTENTIAL ENERGY = -196.7417484352
NUCLEUS-NUCLEUS POTENTIAL ENERGY = 9.0871358664
------------------
TOTAL POTENTIAL ENERGY = -149.5268402806
TOTAL KINETIC ENERGY = 74.5624248550
VIRIAL RATIO (V/T) = 2.0053913291
...... PI ENERGY ANALYSIS ......
ENERGY ANALYSIS:
FOCK ENERGY= -45.9237766278
BARE H ENERGY= -122.1793235802
ELECTRONIC ENERGY = -84.0515501040
KINETIC ENERGY= 74.5624248550
N-N REPULSION= 9.0871358664
TOTAL ENERGY= -74.9644142376
SIGMA PART(1+2)= -76.2127294486
(K,V1,2)= 69.5049624030 -176.7884643168 31.0707724652
PI PART(1+2)= -7.8388206554
(K,V1,2)= 5.0574624520 -19.9532841185 7.0570010110
SIGMA SKELETON, ERROR= -67.1255935822 0.0000000000
MIXED PART= 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00
...... END OF PI ENERGY ANALYSIS ......
---------------------------------------
MULLIKEN AND LOWDIN POPULATION ANALYSES
---------------------------------------
ATOMIC MULLIKEN POPULATION IN EACH MOLECULAR ORBITAL
1 2 3 4 5
2.000000 2.000000 2.000000 2.000000 2.000000
1 2.001361 1.617307 1.068623 1.667555 2.000000
2 -0.000680 0.191347 0.465688 0.166222 0.000000
3 -0.000680 0.191347 0.465688 0.166222 0.000000
----- POPULATIONS IN EACH AO -----
MULLIKEN LOWDIN
1 O 1 S 1.99768 1.99607
2 O 1 S 1.83410 1.68593
3 O 1 X 1.06862 1.09728
4 O 1 Y 2.00000 2.00000
5 O 1 Z 1.45445 1.46728
6 H 2 S 0.82258 0.87672
7 H 3 S 0.82258 0.87672
----- MULLIKEN ATOMIC OVERLAP POPULATIONS -----
(OFF-DIAGONAL ELEMENTS NEED TO BE MULTIPLIED BY 2)
1 2 3
1 7.8326767
2 0.2610849 0.6079246
3 0.2610849 -0.0464327 0.6079246
TOTAL MULLIKEN AND LOWDIN ATOMIC POPULATIONS
ATOM MULL.POP. CHARGE LOW.POP. CHARGE
1 O 8.354846 -0.354846 8.246557 -0.246557
2 H 0.822577 0.177423 0.876722 0.123278
3 H 0.822577 0.177423 0.876722 0.123278
-------------------------------
BOND ORDER AND VALENCE ANALYSIS BOND ORDER THRESHOLD=0.050
-------------------------------
BOND BOND BOND
ATOM PAIR DIST ORDER ATOM PAIR DIST ORDER ATOM PAIR DIST ORDER
1 2 0.969 0.957 1 3 0.969 0.957
TOTAL BONDED FREE
ATOM VALENCE VALENCE VALENCE
1 O 1.913 1.913 0.000
2 H 0.969 0.969 0.000
3 H 0.969 0.969 0.000
---------------------
ELECTROSTATIC MOMENTS
---------------------
POINT 1 X Y Z (BOHR) CHARGE
0.000000 0.000000 0.000026 0.00 (A.U.)
DX DY DZ /D/ (DEBYE)
0.000000 0.000000 1.713972 1.713972
...... END OF PROPERTY EVALUATION ......
CPU 0: STEP CPU TIME= 0.02 TOTAL CPU TIME= 0.1 ( 0.0 MIN)
TOTAL WALL CLOCK TIME= 0.1 SECONDS, CPU UTILIZATION IS 81.91%
580000 WORDS OF DYNAMIC MEMORY USED
EXECUTION OF GAMESS TERMINATED NORMALLY Mon Apr 11 13:58:57 2011
DDI: 263224 bytes (0.3 MB / 0 MWords) used by master data server.
----------------------------------------
CPU timing information for all processes
========================================
0: 0.171 + 0.62 = 0.233
1: 0.140 + 0.00 = 0.140
2: 0.00 + 0.15 = 0.15
3: 0.00 + 0.31 = 0.31
----------------------------------------
ddikick.x: exited gracefully.
----- accounting info -----
Questions¶
INPUT CARD
The INPUT CARD section at the start shows the first few lines of the input file. Here it shows the entire input.
- Can you figure out from the input file that this is a RHF/STO-3G calculation?
- The input file appears to only specify the coordinates for two atoms, an oxygen and a hydrogen. How does GAMESS know that there is a second hydrogen? (Hint: see the section after
RUN TITLE.)
INTERNUCLEAR DISTANCES
- In the
INTERNUCELAR DISTANCESsection, what is the point of the asterisks after some of the distance values?
ATOMIC BASIS SET
- How many basis functions are there? Can you work out what basis functions they are? (Hint: see the
EIGENVECTORSsection.) - How many occupied orbitals are there?
- Neutral water has 10 electrons, and a spin multiplicity (number of unpaired electrons + 1) of 1. If a molecule had 11 electrons, what values for multiplicity would be possible?
$SYSTEM OPTIONS
The amount of memory available to GAMESS can be set using the MWORDS command (megawords) in the $SYSTEM section. The value of MWORDS defaults to 1 (i.e. 1000000 words).
- If 1 word is 8 bytes, how many MB of memory are available to GAMESS by default? Given that modern computers have 2GB or more of RAM, is it safe to increase this value if GAMESS complains about running out of memory?
RHF SCF CALCULATIONS
Much of the computation time in a typical calculation is spent in the SCF section. This is an iterative procedure that keeps repeating until the difference between the density matrix on successive iterations is less than 0.00002.
- How many iterations did it take for SCF convergence? What was the final energy?
- Would you say that the SCF converges nicely in this case? What would you expect to see if there was a problem converging the SCF?
- Could you make a guess about the meaning of
MAXIT = 30? Can you think of any circumstance where it might be useful to increase this value?
EIGENVECTORS
The eigenvectors of a QM calculation are the molecular orbitals. Each molecular orbital is described in terms of the basis functions.
- How many molecular orbitals are there?
- Which eigenvector represents the HOMO? What is its energy? Where is the HOMO located?
- Which eigenvector represents the LUMO? What is its energy?
MULLIKEN AND LOWDIN POPULATION ANALYSES
- What are the Mulliken charges on each atom? Do they make sense?
Molecular orbitals of water¶
Let’s visualise the molecular orbitals of water at the HF/3-21G level of theory.
Create an initial 3D structure¶
Using Avogadro, we can create an initial structure of the water molecule. Simply choose the Draw Tool (
), change the Element to Oxygen, tick the box for Adjust Hydrogens, and click anywhere in the View Window.
This will draw a single oxygen atom, and hydrogens will be added automatically to satisfy the oxygen atom’s valency, giving H2O.
Now optimise the structure using the MMFF94 forcefield (Extensions/Optimize Geometry).
Generate the GAMESS input file¶
Under Extensions/GAMESS/Input Generator, choose Equilibrium Geometry to find the optimized geometry. Choose RHF for the method and 3-21G for the basis set.
The other options should be left at their default of Gas phase calculation, Singlet multiplicity, and Neutral charge.
Click on Generate... to save the GAMESS input file to an appropriate location.
Run GAMESS¶
Open a Windows folder showing the location of the GAMESS input file. Open another Windows folder showing the location where GAMESS was installed (typically C:/WinGAMESS).
Now drag-and-drop the GAMESS input file on top of C:/WinGAMESS/WG_DDE.BAT.
This will start the calculation, and the output will be written to a file with the same name and location as the input file, but with the extension .out.
Investigate the geometry optimisation¶
Start wxMacMolPlt, and File/Open the output file from the GAMESS run.
The geometry optimisation probably involved several steps. You can use the slider at the bottom right of the wxMacMolPlot window to investigate the steps.
If you click on Subwindow/Energy Plot you can see a plot of the energy values and root-mean-squared change in coordinates for the steps.
Look at the electrostatic potential¶
The molecular electrostatic potential (MEP) is a measure of the force (attractive or repulsive) felt by a point charge at a certain point in space due to the electronic distribution in a molecule. We can colour the molecular surface using the MEP to give some idea of where nucleophiles or electrophiles might attack.
Here we will use an isosurface of the electron density to represent the molecular surface.
Click on Subwindow/Surfaces/”3D Total Electron Density”. Click Update to generate a wireframe wire of an isosurface of the electron density.
Note
What the effect of increasing or decreasing the number of grid points, the grid size, or the contour value?
It is worth remembering that the larger the contour value, the smaller the volume contained by the isosurface.
Set the number of grid points to 25, the counter value to 0.04, the Surface Display to Solid, tick the Smooth box and click Update.
To colour the surface using the MEP, tick “Colorize using the surface MEP value” and also “Invert color map”. You may want to increase the Transparency to 20%, then click Update.
When finished admiring your work, click Delete to remove the surface.
Visualise the orbitals¶
Now click Add.../”3D Orbital” to bring up the orbital visualiser settings.
Draw the HOMO using a smooth solid surface. Save a copy of the view using File/Export. Choose “Portable Network Graphics (*.png)”, the filename water_homo.png and click Save. In the Export Options, choose “300dpi (Print)”.
Do the same for the LUMO. How do they compare?
Vibrational frequencies of water¶
Vibrational frequency calculations should always be carried out to verify that a geometry optimisation has found a true minimum, and not just a saddle point.
They are also useful in their own right to find and visualise the normal modes of vibration.
Create the GAMESS input file and run GAMESS¶
The vibrational frequencies are only valid at an optimised geometry so we need to use the geometry obtained in the previous calculation.
To open a GAMESS output file in Avogadro, we need to first rename it from .out to .gamout. Once this is done, use File/Open in Avogadro to open the file.
Next click Extensions/GAMESS/”Input Generator” and choose “Frequencies” under Calculate. Click on Generate and save the GAMESS input file.
Run GAMESS using drag-and-drop as before.
Analyse the frequencies¶
It is worth opening the GAMESS output file in Wordpad and taking a look at the NORMAL COORDINATE ANALYSIS section (see below). (Hint: In Wordpad, it is useful to “Select All” and change the font size to 8 pt.)
- Is this molecule at a true geometry minimum?
- How many frequencies are expected for a 3-atom non-linear molecule? (Hint: 3N-6)
- How many frequencies are present in the file? How can you account for the difference?
--------------------------------------------------------
NORMAL COORDINATE ANALYSIS IN THE HARMONIC APPROXIMATION
--------------------------------------------------------
ATOMIC WEIGHTS (AMU)
1 O 15.99491
2 H 1.00782
3 H 1.00782
MODES 1 TO 6 ARE TAKEN AS ROTATIONS AND TRANSLATIONS.
ANALYZING SYMMETRY OF NORMAL MODES...
FREQUENCIES IN CM**-1, IR INTENSITIES IN DEBYE**2/AMU-ANGSTROM**2,
REDUCED MASSES IN AMU.
1 2 3 4 5
FREQUENCY: 1.33 0.16 0.00 0.33 6.17
SYMMETRY: A A A A A
REDUCED MASS: 1.01401 6.22305 6.00353 12.81051 1.03666
IR INTENSITY: 8.39984 0.00224 0.00000 0.52570 3.14657
1 O X -0.00000000 -0.04742972 0.23101688 -0.00000000 0.03749320
Y -0.00000000 0.23166471 0.04641338 -0.00000000 -0.02121402
Z -0.02017373 0.00000000 0.00000000 0.24794115 -0.00000000
2 H X -0.00000000 -0.04712588 0.23101681 -0.00000000 0.02610283
Y 0.00000000 0.21251345 0.04641346 -0.00000000 0.69693540
Z 0.87470814 0.00000000 0.00000000 0.02267176 -0.00000000
3 H X -0.00000000 -0.02927595 0.23101629 -0.00000000 -0.64326004
Y -0.00000000 0.23777094 0.04641325 -0.00000000 -0.25019888
Z 0.46974713 0.00000000 0.00000000 0.12677581 -0.00000000
TRANS. SAYVETZ X -0.00000000 -0.83563375 4.16074267 -0.00000000 -0.02228604
Y -0.00000000 4.15926402 0.83593088 -0.00000000 0.11091595
Z 1.03229856 0.00000000 0.00000000 4.11641335 -0.00000000
TOTAL 1.03229856 4.24237681 4.24388501 4.11641335 0.11313273
ROT. SAYVETZ X 0.74353714 -0.00000000 -0.00000000 -0.18361186 -0.00000000
Y -1.26256812 0.00000000 0.00000000 0.31924861 0.00000000
Z 0.00000000 -0.06777613 0.00000119 0.00000000 2.54154460
TOTAL 1.46523914 0.06777613 0.00000119 0.36828385 2.54154460
6 7 8 9
FREQUENCY: 8.88 1799.28 3812.34 3945.80
SYMMETRY: A A A A
REDUCED MASS: 1.01756 1.08983 1.03858 1.08500
IR INTENSITY: 0.86226 1.89217 0.00115 0.21702
1 O X 0.00000000 -0.04089486 -0.02564877 -0.05626299
Y -0.00000000 -0.05786491 -0.03630837 0.03975514
Z -0.02526058 0.00000000 -0.00000000 -0.00000000
2 H X 0.00000000 0.01882370 0.69075509 0.67710255
Y 0.00000000 0.67521698 -0.05628041 0.01073177
Z -0.47603300 0.00000000 -0.00000000 0.00000000
3 H X -0.00000000 0.63020849 -0.28369066 0.21583219
Y -0.00000000 0.24314193 0.63252054 -0.64167502
Z 0.86919577 -0.00000000 -0.00000000 0.00000000
TRANS. SAYVETZ X -0.00000000 0.00000129 -0.00000014 0.00000052
Y 0.00000000 0.00000111 0.00000004 -0.00000057
Z -0.00780139 0.00000000 -0.00000000 0.00000000
TOTAL 0.00780139 0.00000170 0.00000015 0.00000077
ROT. SAYVETZ X 1.50357589 -0.00000000 0.00000000 0.00000000
Y 1.38590886 -0.00000000 0.00000000 -0.00000000
Z 0.00000000 -0.00001496 -0.00000000 0.00000153
TOTAL 2.04486768 0.00001496 0.00000000 0.00000153
REFERENCE ON SAYVETZ CONDITIONS - A. SAYVETZ, J.CHEM.PHYS., 7, 383-389(1939).
NOTE - THE MODES J,K ARE ORTHONORMALIZED ACCORDING TO
SUM ON I M(I) * (X(I,J)*X(I,K) + Y(I,J)*Y(I,K) + Z(I,J)*Z(I,K)) = DELTA(J,K)
-------------------------------
THERMOCHEMISTRY AT T= 298.15 K
-------------------------------
USING IDEAL GAS, RIGID ROTOR, HARMONIC NORMAL MODE APPROXIMATIONS.
P= 1.01325E+05 PASCAL.
ALL FREQUENCIES ARE SCALED BY 1.00000
THE MOMENTS OF INERTIA ARE (IN AMU*BOHR**2)
2.07948 4.38456 6.46404
THE ROTATIONAL SYMMETRY NUMBER IS 1.0
THE ROTATIONAL CONSTANTS ARE (IN GHZ)
867.08597 411.23564 278.94127
THE HARMONIC ZERO POINT ENERGY IS (SCALED BY 1.000)
0.021773 HARTREE/MOLECULE 4778.712676 CM**-1/MOLECULE
13.663039 KCAL/MOL 57.166155 KJ/MOL
Q LN Q
ELEC. 1.00000E+00 0.000000
TRANS. 3.00431E+06 14.915558
ROT. 8.69029E+01 4.464791
VIB. 1.00017E+00 0.000170
TOT. 2.61127E+08 19.380518
E H G CV CP S
KJ/MOL KJ/MOL KJ/MOL J/MOL-K J/MOL-K J/MOL-K
ELEC. 0.000 0.000 0.000 0.000 0.000 0.000
TRANS. 3.718 6.197 -36.975 12.472 20.786 144.800
ROT. 3.718 3.718 -11.068 12.472 12.472 49.594
VIB. 57.170 57.170 57.166 0.106 0.106 0.014
TOTAL 64.607 67.086 9.123 25.050 33.364 194.407
VIB. THERMAL CORRECTION E(T)-E(0) = H(T)-H(0) = 3.649 J/MOL
E H G CV CP S
KCAL/MOL KCAL/MOL KCAL/MOL CAL/MOL-K CAL/MOL-K CAL/MOL-K
ELEC. 0.000 0.000 0.000 0.000 0.000 0.000
TRANS. 0.889 1.481 -8.837 2.981 4.968 34.608
ROT. 0.889 0.889 -2.645 2.981 2.981 11.853
VIB. 13.664 13.664 13.663 0.025 0.025 0.003
TOTAL 15.441 16.034 2.180 5.987 7.974 46.464
VIB. THERMAL CORRECTION E(T)-E(0) = H(T)-H(0) = 0.872 CAL/MOL
......END OF NORMAL COORDINATE ANALYSIS......
Visualise the normal modes¶
Open the output file in wxMacMolPlt. List the normal modes with Subwindow/Frequencies.
If you click on any mode, the main window will update to show you the displacement vectors associated with it. You can animate the vibration with View/Animate Mode.
Effect of basis set¶
We are going to compare the effects of the basis set on the energy of a RHF calculation on water.
Running GAMESS¶
To speed things up, we are going to use the geometry we found for RHF/3-21G and use that for our calculations.
In Avogadro, open the output file from the RHF/3-21G geometry optimisation of water (remember to rename the file to .gamout), and create several input files for a single-point RHF calculations with increasing basis set size.
The notation for calculations of this type uses the // notation; for example, RHF/6-31G//RHF/3-21G.
When they have all been created, run each of them in turn.
(Note to self: Is there time to run an MP2/3-21G calculation?)
Analyse¶
For each calculation, note the final RHF energy and also the wall clock time (found at the end of the output file).
- What is the effect of the basis set size on the energy? Based on this, does it make sense to compare the results of calculations with different basis set sizes?
- What is the effect of the basis set size on the computation speed?
Conformations of a cyclohexane¶
The geometry optimsation procedures in QM software involve local optimisation of the energy, not global optimisation. This allows us to investigate energy differences between different conformations.
We are going to look at the difference in energy between conformations of 1,4-dichloro-cyclohexane.
Create an initial structure¶
Under Build/Insert/Fragment, choose share/avogadro/fragments/cyclic alkanes/cyclohexane.cml. Click Insert Fragment. Choose Edit/Select None to clear the selection.
Note
Which conformation of cyclohexane is this?
Choose the Draw Tool (), and change any hydrogen to a chlorine. Find the hydrogen atom on the opposite carbon that is on the same face of the ring, and change this also to chlorine.
Optimize the geometry using MMFF94.
Note
What parts of the structure change?
Generate conformations interactively¶
Click on the Auto Optimization Tool (
) and choose Start to turn it on. (Make sure that it is using the MMFF94 forcefield.)
Click on one of the chlorine atoms and drag it to change to another conformation.
Note
How many conformations of this cyclohexane can you find?
For each conformation:
- use the Measure Tool (
) to measure the chlorine-chlorine distance - use Extensions/Molecular Mechanics/Calculate Energy to find the MMFF94 energy
- save each conformation to a CML file
Turn off the Auto Optimization by clicking Stop.
Calculate accurate energies¶
Open the saved conformations one-by-one, and generate input files for GAMESS for a geometry optimisation at the HF/3-21G level of theory.
Carry out the calculation for each conformation and note the energy.
Note
Is the same trend in energies observed for MMFF94 and HF/3-21G?