Using the CCP1GUI to run a Geometry Optimisation calculation on
salicyclic acid using GAMESS-UK.
This tutorial will go through all the steps you need to go through
to use the CCP1GUI to run a geometry optimisation on
salicylic acid using GAMESS-UK. The tutorial will take you through
the steps need to draw the salicylic acid molecule with the GUI and then use
the grapical interface to GAMESS-UK to carry out the calculation.
The first step is to start up the GUI (for instructions on how to
install the gui, follow this
For the purposes of this tutorial, the place where the GUI is
installed (the top-level directory for the GUI) will be referred to as
$CCP1GUIDIR. If you have the GUI installed in the
directory: /home/john/software/ccp1gui, for example,
substitute this for the line $CCP1GUIDIR wherever you
see it in this tutorial.
To start up the GUI under Windows, double-click on the ccp1gui.bat
file that sits in the $CCP1GUIDIR. To start
the GUI under Linux or Unix, run the ccp1gui.bash script that can be
found in $CCP1GUIDIR. The script is run by typing:
and then hitting return.
You should then see the following:
|Screenshot 1: The CCP1GUI main window|
Creating the salicyclic acid molecule
As we will be creating a molecule from scratch, the first step is
to create a new molecule. To do this select File -> New
Molecule from the main menu at the top of the GUI window (referred
to as the main window from here on).
|Screenshot 2: Selecting a New Molecule|
Two things will happen when you do this. An sp3-hybridised carbon
atom with 4 X (i.e. unidentified) atoms will apear in the main window and the
Editing Tool Panel (referred to as the tool panel from
here on) will appear as a separate window floating just below the main
|Screenshot 3: The New Molecule|
|Screenshot 4: The Editing Tool Panel|
As a first step we wil add a benzene ring to one of the X-atoms
using the Add Fragment tool in the tool panel. Select any one of
the X-atoms by clicking on it with the left mouse buttun (a yellow dot
will appear over the atom indicating it has been selected). Now select
Ph from the Add: menu (bottom right of the tool
panel). This will add a phenyl-fragment to the X-atom and convert it
to a carbon atom.
|Screenshot 5: Adding a Phenyl Fragment|
If the molecule is no longer centered on the screen or is oriented
incorrectly, you can either:
- Drag the molecule into the centre of the screen.
- To do this Click
and hold the middle mouse button. This grabs the
molecule and you can then drag it wherever you wish on the main
window. Releasing the middle mouse button releases the molecule.
- Zoom in or out until the whole molecule fits into the screen.
- To do this click and hold the right mouse button and move the
mouse forwards (towards the screen) to zoom in, or backwards to move
- Rotate the molecule into a better orientation.
- To do this Click and hold the left mouse button and move
the mouse around to change the orientation of the molecule.
- Centre the molecule on particular atom.
- To do this, click on a atom that you would like to centre the molecule on and then select Views -> Centre on Selected
The main window should now look something like this:
Having added the benzene ring, the next stage is to change the
remaining -CX3 moiety into a carboxylic acid group. This
requires changing the hybridisation of the carbon atom to sp2, so that
the oxygen atom can be attached to it via a double-bond. Select the
carbon atom and then click the sp2 button in the
hybridisation section of the toolbar. This will convert the
-CX3 moiety sp3 hydridised moiety to a -CX2 sp2
hybridised planar moiety.
|Screenshot 6: The added Phenyl Fragment|
To convert both of the X-atoms to oxygen atoms, click on them both
with the left mouse button and then click on the O atom type in
the Change Element Type section of the toolbar (if you
accidently select the wrong atoms clicking on a blank area of the main
window will de-select all the currently selected atoms). This has
created the CO2 group attached to the benzene ring.
With the two X atoms changed to oxygen, a hyrdogen atom needs to be
added to one of them. The easiest way to do this is to hybridise one of
the oxygens to sp2, delete one of the X-atoms that is created and then
change the remaining X to an oxygen. To do this, click on one of the oxygen
atoms and click sp2 from the hydbridisation section of
the editing toolbar to create two X-atoms. Select the one
the one you would like to delete and click on the Del Atom
editing toolbar as shown below:
|Screenshot 7: Changing the X's to Oxygens|
Now change use the Change Element Type button on the toolbar
to change the X atom to an oxygen atom.
|Screenshot 7: Changing the X's to Oxygens|
The final stage in the process of creating the molecule is to
replace the H atom next to the CO2 moeity on the benzene
ring with an OH group. To do
this, select the H-atom with the mouse and use the
Change Element Type section of the editing toolbar to change its type
to oxygen. Then click on the sp2 button to change it's
hybridisation to sp2, delete one of the X-atoms that is created with
the Delete Atom button and use the Change Element Type
button to change the remaining X to an oxygen.
The molecule should now look like this:
This completes the creation of the molecule. The GUI will have
created the molecule using cartesian coordinates. As the first
GAMESS-UK calculation we will be running optimises the
geometry of the molecule, we need to convert
the cartesian coordinates of the salicyclic acid molecule into z-matrix form
suitable for a geometry optimisation.
|Screenshot 8: The completed salicyclic acid molecule|
Changing to Internal (Z-matrix) coordinates
Changing the coodinates of a molecule in the CCP1GUI is carried out
using the Z-Matrix Editor tool. The Z-matrix Editor is accessed
by selecting Edit -> Edit Coords in the main window. This
causes the Z-matrix editor to appear in a seperate window to the left
of the main window.
|Screenshot 7: Selecting the Coordinate Editor|
|Screenshot 8: The Z-matrix Editor|
To convert the whole molecule to internal coordinate form, select
Convert -> Autoz from the menu at the top of the
z-matrix editor. This will automatically generate the internal
Creating Variables to be optimised
Although this has generated the required internal coordinates, we
have not selected any variables (bond lengths or angles) that we would
like to optimise. For the purposes of this optimisation we are going
optimise all the C-O bond length of the OH group attached to the
To select the C-O bond as a variable, click on the oxygen in the
main window and the relevant line will become highlighted in the
Z-matrix window. Next, select Edit -> "r,x ->
var", which will convert the r (bond length) to
a variable, so that it appears in the variables window to the bottom
left of the z-matrix editor. The names and initial values of the
any variable can be altered by clicking on the variable in the
varables window and then changing either the name or the value in the
boxes just below the variables window.
|Screenshot 9: Selecting the Bond Length Variable for the Optimisation|
Having created our z-matrix, it makes sense to save it, so select
File -> Save Z-Matrix and save the file in your working directory
as salicyclic.zmt (make sure you include the .zmt suffix
in the name). With this task completed, close down the
Z-matrix editor by selecting File -> Close.
We are now in a position to run a GAMESS-UK calculation.
Running a closed-shell STO-3G calculation on salicyclic acid
Basic calculation set up
To open up the GAMESS-UK control window, select Compute ->
GAMESS-UK. The window below will be displayed.
|Screenshot 10: The GAMESS-UK Window|
There is a menu bar along the top (Calc, Edit and
View) and a series of window tabs below this (Molecule,
Theory, etc.) that allow you to configure various calculation
To give the calculation a title (which will be displayed at the top
of the text-file that GAMESS-UK generates as it's output) highlight
the text in the title field in the molecule tab and input a title.
As we are running a geometry optimisation calculation, we set the
Task set to Geometry Optimisation. To make sure
that the spin and charge are valid for this molecule click on the
Check Spin. The spin for this molecule should be o.k., but if
it were incorrect you can either enter the correct spin and charge in the
relevant text box, or increment or decrement the values with the
pointers on either side of the text box.
To select the sto-3g basis functions that we will be
using for the calculation, use the Basis Selector group in the
lower half of themolecule tab. As we are applying the same basis
functions to all the atoms in the molecule, we select sto-3g from the
Default Basis menu. You should notice that the Current Basis
Assignment window to the left now shows the sto-3g basis set for
|Screenshot 11: Changing the default basis set|
Controlling the SCF calculation
With the molecule set up, the next stage is to take a bit more
control over the nature of the scf calculation to be carried out. This is
done with the tools in the Theory tab.
|Screenshot 12: The GAMESS-UK Theory Tab|
As this is the first calculation, and we are carrying out an RHF
calculation, the defaults should suffice.
NB: For more information on the
individual options that are available in a particular tab you can activate balloon help (this option is found under the Help menu on the far right hand side of the CCP1GUI Main window). With balloon help active, hover your mouse over the option you are interested in, and a small description of what it does will appear. Alternatively, to get fuller documentation on any of the features within a tab, either press F1 while the tab you are interested in is displayed, or visit the gamess-uk
Controlling the geometry optimisation
To specify the type and parameters of the geometry optimisation,
click on the Optimisation tab at the top of the GAMESS-UK
|Screenshot 13: The GAMESS-UK Optimisation Tab|
As we are performing this optimisation in internal coordinates,
make sure that Z-Matrix is selected in the Opt. Coords
selector, and that the Locate Transition State box is unchecked
(checking this would perform a transition state search).
The remaining default values should be o.k. For more information on the
individual options, either press F1 while the tab you would like more
information about is displayed, or visit the gamess-uk
Setting up the calculation environment
The final stage for this first calculation is to determine some of
the parameters relating to the environment that the job wil run
in. These are configured in the Job tab.
|Screenshot 14: Setting up the GAMESS-UK job|
The Job Name tab determines the stem that will be
used as the basis of the name for all the files produced by
GAMESS-UK. For the current job, set this to
Setting Host Name to localhost indicates that we are running
the calculation on this computer (as opposed to on a remote one or via
a batch submission system) and this renders the Job Submission
and User irrelevant for this case.
The working directory is where the GAMESS-UK job will run
and where (by default) all the files produced by GAMESS-UK will be
saved. You can use the browse button to select a suitable
If you plan to do any additional calculations on the molecule, it
is advisable to save the GAMESS-UK dumpfile. When GAMESS-UK
runs a standard scf calculation, it creates 3 files as it is
running. These files are ed2, which holds the two-electron
integrals, ed3, which holds various information related to the
state of the calculation (eigenvectors, restart information Hessians,
CI-coefficients etc.) and ed7which holds various housekeeping
information used by the program as it runs. ed3 is called the
dumpfile and the information stored in it can read back in
for a subsequent restart calcualtion. Determing the location of the
ed files (and that they should be kept and not deleted as is the
default)is carried out by the tools in the File Path in
the lower half of the job tab.
To save the dumpfile, click on the keep button. This action makes
the specify button appear. The default action is to save the
dumpfile in the current working directory with a name made up from the
Job Name with the suffix .ed3
appended. To change this to something different, click on the
specify button and select a name/location of your choice.
Running the calculation
Running the calculation is simply a matter of selecting Calc
->Run from menu at the top of the GAMESS-UK window. This
creates a text file containing the GAMESS-UK directives and runs
GAMESS-UK on this file (the input file can be viewed by selecting
View -> Input
When the GUI is running a calculation, a Job Manager will
pop up. This displays the jobs that are running and has a kill
button that can be used to stop jobs that are running. You will need to select the job you would like to kill, so that it is highlighted in the job manager for this to work.
|Screenshot 15: The GAMESS-UK Job Manager|
NB: If you wish to have more control over the input deck for
the GAMESS-UK job (to add extra GAMESS-UK directives that are not
supported by the GUI for instance), select Calc -> Write
InputFile. This causes the GAMESS-UK input file to be created in
the directory specified by the Working Directory tool in the
Job tab with the name specifed by the Job Name tool,
with the suffix .in appended to it. To edit this file, select Edit -> Input from the GAMESS-UK
menu. This brings up the input file in a seperate editor window. You
can move around this window with the mouse or arrow-keys and edit the
sections you choose. Click Save to save your edits to file or
Save As to save this input file with a different name. Clicking
Quit will close the editor window.
To run the File with your edits included, select Calc -> Run
InputFile. DO NOT just click Calc -> Run as this
will create a fresh input file from the options selected in the GUI
and overwrite your amended file.
Viewing the Results of a Calculation
If the calculation proceeds succesfully, the following window will
|Screenshot 16: A successful GAMESS-UK Job Run|
The window will be upated so that the molecule will show any
geometry changes that have occured due to the opimisation. When the
GAMESS-UK run has completed, a file with name specified in the Job
Name field and the suffix .out will be created in the
directory specified as the working directory. To view the
results of the calculation with the GUI, select View -> Output in the
GAMESS-UK window, and the ouput file will be displayed in a separate
|Screenshot 17: The output from a GAMESS-UK Job|
Just click on OK to close this window
Click here to return to the CCP1GUI