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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 link).

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:

ccp1gui.sh

and then hitting return.

You should then see the following:

The Main GUI window
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).

New Molecule
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 window.

New Molecule
Screenshot 3: The New Molecule

Editing Panel
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.

Adding Phenyl
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 out.

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:

Added Phenyl
Screenshot 6: The added Phenyl Fragment
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.

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.

Changing X to O
Screenshot 7: Changing the X's to Oxygens
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:

Changing X to O
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.

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:

Salicyclic molcule
Screenshot 8: The completed salicyclic acid molecule
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.

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.

Selecting Edit Coordinates
Screenshot 7: Selecting the Coordinate Editor

Z-Matrix 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 coordinate representation.

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 benzene ring.

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.

Selecting Bond Length Variables
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.

Gamess Window
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 parameters.

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 all atoms.

Basis Select
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.

Gamess Theory
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 window documentation.

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 window.

Gamess Optimisation
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 window documentation.

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.

GamessJob
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 "salicyclic_sto3g".

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 directory.

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.

GamessJobmanger
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 be displayed:

GamessJobOK
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 window.

GamessCalcRes
Screenshot 17: The output from a GAMESS-UK Job

Just click on OK to close this window


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For more information about the work of the Computational Chemistry Group please contact Paul Sherwood p.sherwood@dl.ac.uk or Bill Smith w.smith@dl.ac.uk
 
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