Tutorial for Windows Systems Exerciso QS.1:Wator ltti1ilr【li Single Point Enorgy Elle Edit Check-Route Set-Start file:qs.gif C:USRAEFRISCHH20.GJF #T RHF/6-31G(d) My first Gausslan Job:water sIngle point cnergy 01 00.4640.1770.0 H0.4641.1370.0 H0.4410.1430.0 The top three icons on the right side of this window can be used to return to the main menu in various ways: Corresponding Icon Action File Menu Option Return to the main menu. Exit Return to the main menu and begin Exit Run executing the job. Discard input and return to the main Abandon Dat menu. 11.Select Exit from the File menu or click on the exit icon with the mouse. This will return you to the main program window.Notice that the Output File display now contains the name of the file where output from this job will go,Water.Out. Output will also appear in the large window below the Run Progress display. Exploring Chemistry with Electronic Structure Methods x精
Exerei•• QS.l: Water 5i~1e Point Energy ·q··gtf Tutorial for Windows Systems o -0.464 0.117 0.0 H -0.464 1.137 0.0 H 0.441 -0.143 0.0 The top three icons on the right side ofthis window can be used to return to the main menu in various ways: Return to the main menu. Exit Return to the main menu and begin Exit & Run executing the job. Discard input and return to the main Abandon Data menu. Icon II II II Action Corresponding File Menu Option 11. Seled Exit from the File menu or click on the exit icon with the mou.e. This will return you to the main program window. Notice that the Output File display now contains the name of the file where output from this job will go, Water.Out. Output will also appear in the large window below the Run Progre.. display. Exploring Chemistry with Electronic Structure Methods xliii
Quick Running Gaussian Start Gaussian 94W jobs may be started in two ways: The Run icon By pressing the Run icon By selecting Begin Processing from the Process menu. 12. Start your water energy calculation in one of these ways. As the calculation proceeds,the Run Progress display line will be periodically updated to indicate how the job is progressing.Here is a typical display: C:G94WL301.exe ls processing.. This line indicates that the job is currently executing Link 301.All versions of Gaussian are divided into approximately 75 modules known as links,having namesof the form Lnnn where nnn is a one to four digit number.As you gain experience,many of these links will become familiar to you. To aid you in this process,a description of the current link appears in the status display at the bottom of the screen while a job is running: You may pause or terminate a running job by using items from the Process menu or their corresponding icons: Corresponding Icon Action Process Menu Item Immediately pause job. Pause Pause after the current link. Pause Next Link Resume executing a paused job. Resume Terminate the current job. K湖ob Output is added to the output display area as it is produced by the program.This area is horizontally and vertically scrollable and may be examined at any point throughout job execution. xliv Exploring Chemistry with Electronic Structure Methods
xliv Exploring Chemistry with Electronic Structure Methods 12. Start your water energy calculation in one of these ways. Kill Job Resume Pause Pause 0 Next link Corresponding Process Menu Item C:\G94:W\L3Dl.exe Is processing••• ,·.~.~_~~ __~~m__~~~~ • .. By pressing the Run icon .. By selecting Begin Processing from the Process menu. Icon Action 1]1 Immediately pause job. [II Pause after the current link. lD Resume executing a paused job. [III Terminate the current job. T __ .... ~'.'__ "'" .0 ••••••• ~" • • • T' • T' .. • _ • '~ "'"""""«< ,,:2=',. "'"" ......" ""'~:-: "~~;:;~h ',1/:tf ,....,~:'~,::;::'" "/"~' A / 8' "' , r "'~,~..... __..._""""" .N,." '-'- ""_,,,,~,," _,. n_ _ , You may pause or terminate a running job by using items from the Proc•• menu or their corresponding icons: Output is added to the output display area as it is produced by the program. This area is horizontally and vertically scrollable and may be examined at any point throughout job execution. To aid you in this process, a description of the current link appears in the statui display at the bottom ofthe screen while a job is running: This line indicates that the job is currently executing Link 301. All versions of Gaussian are divided into approximately 75 modules known as links, having names of the form lnnn where nnn is a one to four digit number. As you gain experience, many ofthese links will become familiar to you. As the calculation proceeds, the Run Progress display line will be periodically updated to indicate how the job is progressing. Here is a typical display: Gaussian 94W jobs may be started in two ways: Running Gaussian I h Rvn icon III Quick Start
Tutorial for Windows Systems When the job finishes,the Run Progress area displays this message: Pc Complete. The output window still contains the output from the job.We'll look at it briefly now and in more detail a bit later. 13.Examine the job output,and locate the following lines near the end of the output window: Job cpu time:0 days 0 hours 0 minutes 12.6 seconds. File lengths (MBytes):RWF=5 Int=1 D2E=0 Chk=1 Scr=0 Normal termination of Gaussian 94. This display indicates that the job was successful.It also shows some statistics about resource usage by the job. 14.Move back through the output until you find the line containing "SCF Done." It is located approximately three screens back from the end of the output: SCF Done:E(RHF)=-76.0098706218 A.U.after 6 cycles This is the one of the quantities predicted by this calculation.It indicates that the energy of the system,computed at the Hartree-Fock level,is about -76.00987 hartrees. Converting a Structure from a Graphics Program Exercise QS.2:Converting a PDB File file:water.pdb Input for Gaussian 94W can be created in many different ways: Via the Job Entry window. ◆ As a text file created with any editor,using the same format used by other Gaussian versions (discussed in the previous section). ◆ By converting output from a drawing program and then editing the generated input. We'll look at a simple example of the latter method here,converting the water molecule structure saved in Brookhaven Protein Data Bank(PDB)format. Exploring Chemistry with Electronic Structure Methods x
-------------- Tutorial for Windows Systems When the job finishes, the Run Progress area displays this message: Processing Complete. The output window still contains the output from the job. We'll look at it briefly now and in more detail a bit later. 13. Examine the iob output, and locate the following lines near the end of the output window: Job cpu time: 0 days 0 hours 0 minutes 12.6 seconds. File lengths (MBytes): RWF= 5 Int= 1 D2E= 0 Chk= 1 Scr= 0 Normal termination of Gaussian 94. This display indicates that the job was successful. It also shows some statistics about resource usage by the job. 14. Move back through the output until you find the line containing "SCF Done.1# It is located approximately three screens back from the end of the output: SCF Done: E(RHF) = -76.0098706218 A.U. after 6 cycles This is the one of the quantities predicted by this calculation. It indicates that the energy of the system, computed at the Hartree-Fock level, is about -76.00987 hartrees. Converting a Structure from a Graphics Program Ex.rci.. QS.2: Converting a PDB File file: water.pdb Input for Gaussian 94W can be created in many different ways: .. Via the Job Entry window. .. As a text file created with any editor, using the same format used by other Gaussian versions (discussed in the previous section). .. By converting output from a drawing program and then editing the generated input. We'll look at a simple example of the latter method here, converting the water molecule structure saved in Brookhaven Protein Data Bank (PDB) format. Exploring Chemistry with Electronic Structure Methods
Quick Running Gaussian Start 15.Select the Open...option from the File menu. This option is used to open existing input files and to convert files in other formats to Gaussian input.We're going to convert a file saved in Brookhaven Protein Data Bank (PDB)format. Once you have selected this option,a file selection dialog box will appear: ma或o.pd尚 Select the desired file w.ler idh c from this list box. 阁3w tutor quick Specity file type. Brookhaven [PDB)Files The menu in the lower right part of the dialog box allows you to specify the type of file that you want to open.This setting defaults to Gaussian 94W input files. 16. Select Brookhaven (PDB)Files from the List files of type menu,and then opon the file water.pdb, located in the quick subdirectory. The NewZMat File Conversion window will appear: File to be converted. Select new file for conversion. Nrw.Mat le f oer.ion Prepare converted file C:USREFRISCHWATERPDB or线ecution, Open Job Entry window Name for the resulting after comverling. Gaussian input file. WATER.GJF Open the comverted file in an external editor. Set conversion parameters. Begin conversion. Cancel the conversion. xlvi Exploring Chemistry with Electronic Structure Methods
Quick Start II Running Gaussian 15. Select the Open••• option from the File menu. This option is used to open existing input files and to convert files in other formats to Gaussian input. We're going to convert a file saved in Brookhaven Protein Data Bank 1 (PDB) format. Once you have selected this option, a file selection dialog box will appear: Select the desired file--- from this ~st box. Specify file type.-- The menu in the lower right part of the dialog box allows you to specify the type of file that you want to open. This setting defaults to Gaussian 94W input files. 1 16. Select Brookhaven (PDBI Files from the List files of type menu, and then open the fil. water .pdb, I' located in the quick subdirectory. The NewZMat File Conversion window will appear: File 10 be converted. Select new file for conversion. Name for the resulting GCJussian input file. Set conversion parameters. conYer1ed "Ie for execution. Open Job En!'Y window after convwting. Open .... COft\WIIId file in on external "lor. Begin COfW.-sion. Cancel the COfWenfon. I· I i xlvi Exploring Chemistry with Electronic Structure Methods
Tutorial for Windows Systems This window controls how the generated file is made.The default filename is the same as that of the input file,with the extension.GJF. 17.Make sure that both the Load Generated File and Edit Generated File options are checked, and then click the Convert button. The first of these options loads the created input into memory in preparation for execution by Gaussian 94W.The second one automatically opens the Job Entry window with the generated input. The NewZMat utility will convert the file,and then open the Job Entry window. Notice that NewZMat has set up a Hartree-Fock calculation using the 6-31G(d)basis set by default.The molecule specification in the generated file is also in Z-matrix format rather than Cartesian coordinates.See Appendix B for details on the Z-matrix molecule specification format. 18.Create a title,specify terse output with #T,and then save the file by selecting Save from the File menu. We could now begin executing this job by selecting Exit Run option from the Fle menu.However,don't do that now.Instead,we'll run this job using a different technique in the next subsection. 19.Select Exit from the File menu to return to the main program window. Drag-and-Drop Execution Gaussian 94W provides another quick way of running a job.If an input file has already been prepared,then you can use the drag-and-drop method of running it.It involves these steps(in Windows 3.1): Open the Windows File Manager and locate the desired input file by selecting its directory in the left side of the window and locating it in the list box on the right side. Start Gaussian 94W if it is not already running.The main program window may be open,or the application may be iconified,but no job should be currently running. Select and drag the desired input file from the File Monoger into the Gaussian 94W main program window or on top of its minimized icon.The Exploring Chemistry with Electronic Structure Methods xhi
Tutorial for Windows Systems This window controls how the generated me is made. The default fJ.1ename is the same as that ofthe input ftle, with the extension .GJF. 17. Make sure that both the Load Generated File and Edit Generated File optionl are checked, and then click the Convert button. The first of these options loads the created input into memory in preparation for execution by Gaussian 94'W: The second one automatically opens the Job Entry window with the generated input. The NewZMat utility will convert the file, and then open the Job Entry window. Notice that NewZMat has set up a Hartree-Fock calculation using the 6-31G(d) basis set by default. The molecule specification in the generated fJ.1e is also in Z-matrix format rather than Cartesian coordinates. See Appendix Bfor details on the Z-matrix molecule specification format. 18. Create a title, specify ter.e output with #T, and then lave the file by ..leding Save from the File menu. We could now begin executing this job by selecting Exit & Run option from the file menu. However, don't do that now. Instead, we'll run this job using a different technique in the next subsection. 19. Seled Exit from the File menu to retum to the main program window. Drag-and-Drop Execution Gaussian 94W provides another quick way of running a job. If an input file has already been prepared, then you can use the drag-and-drop method of running it. It involves these steps (in Windows 3.1): • Open the Windows File Manager and locate the desired input file by selecting its directory in the left side ofthe window and locating it in the list box on the right side. • Start Gaussian 94W if it is not already running. The main program window may be open, or the application may be iconified, but no job should be currently running. • Select and drag the desired input file from the file Manager into the Gaussian 94W main program window or on top of its minimized icon. The Exploring Chemistry with Electronic Structure Methods xIYH