Sample Jaguar Calculation
This section provides instructions for running a sample calculation on the water molecule. The sample calculation runs only if Jaguar has been correctly installed. If the calculation does not run, see your system manager or the person who installed Jaguar at your site. Contact Schrödinger if you cannot resolve the installation problems.
First, log on to a machine where the Maestro and Jaguar software is installed, and start Maestro according to the instructions in Running Schrödinger Applications from the Command Line. Once Maestro is running: click the Tasks button and browse to Quantum Mechanics → Single Point Energy to open the Jaguar panel for a single point energy calculation.
The next step is to read in a molecular geometry (structure). Click the button below to download ene-default-0001.in:
To read in the structure, choose Read from the Job Settings button menu (gear icon) at the foot of the panel, then navigate to where ene-default-0001.in has been downloaded saved. Select ene-default-0001.in from the file list, and click OK.
When you finish setting up your calculation, click the Settings (gear) button. The Job Settings dialog box is displayed. In this dialog box you can make settings for running the job. In the Output section, you can select an option for incorporation of results. Choose Replace existing entries.
In the Job section, you can provide a job name, select the execution host, the number of processors, and the scratch directory. The entry name, ene-default-0001, appears in the Name text box. The names of the input, output, and log files for your job depend on the name you provide: the Jaguar input file is named jobname.in, the output file is named jobname.out, and the log file is named jobname.log, where jobname is the text that appears in the Name text box.
The default execution host (the machine that the job will run on) is selected in the Host option menu. This default is localhost, which means the machine on which Maestro is running. The host name is followed by the number of available processors in parentheses. If Jaguar is installed on more than one machine at your site, you can change the choice of execution host by selecting another host from the option menu. The Scratch directory option menu displays the directory on the execution host that will be used during the calculation to store temporary files. You should check that the directory already exists on the execution host. If it does not exist, you should create it.
You should not need to change any other settings. Click the Run button to start the job.
When the job finishes, its output file is copied to a subdirectory of the directory from which you started Maestro, named by the job name. The output file ends with the extension .out. For instance, if you entered the job name h2o, the output file would be h2o.out and would be in the h2o subdirectory.
If you want to exit Maestro, choose File → QuitFile → Quit in the Maestro main window. A dialog box opens, prompting you to save the scratch project. For this exercise, click Discard to discard the scratch project.
To check that the job ran correctly, you can compare the output file produced by the job with ene-default-0001.out:
If you are satisfied with the results of this sample run, proceed to The Jaguar Panel to learn more about using Maestro.