Getting StartedThe WebMO computational chemistry package facilitates computational chemistry on the WWW. WebMO permits the access of various computational chemistry packages over the WWW using only a web browser. Computational chemistry jobs can be created, queued, run, viewed, downloaded, and deleted without the hassle of a UNIX shell. It is even possible to import existing jobs to be viewed within the context of the WebMO interface.
Completed jobs can be viewed by clicking the View button next to the corresponding job. Likewise, the raw output from a failed job can be viewed by clicking the "Raw Output" button next to the job.Queued or running jobs can be aborted or removed from the queue by clicking the "Kill" button next to the corresponding job.
Outdated jobs can be deleted by first selecting the checkbox next to the job(s), and then clicking the "Delete" button at the bottom of the page. Similarly, jobs can be downloaded by first selecting the checkbox next to the job(s), and then clicking the "Download" button at the bottom of the page. A spreadsheet summary of jobs can be created by selecting the desired jobs and clicking the "Spreadsheet" button at the bottom of the page (WebMO Pro only).
Building a MoleculeAfter clicking "Create New Job" in the job manager, you will be brought to the Build Molecule page. This is where you will construct the molecule on which calculations will be carried out. To open the WebMO editor, simply click the "Open Editor" button; use the editor to build the desired molecule, and then close the editor.
Import an Existing MoleculeAlternatively, you may import an existing molecule from an existing file in a variety of formats (MOL, PDB, XYZ, Gaussian style, Mopac style). Simply click the 'Import Molecule' button, select the file format and file name (or paste the contents into the provided text box). To automatically generate bonds between atoms, select the 'Generate Bonds' checkbox. Click the 'Import' button to finish the import process.
When the molecule is complete, click the right arrow at the bottom of the page to move to the next step.
Choose Computational EngineNext, you will be brought to the Choose Computational Engine page. This is where you will choose the computational package which will be used to run calculations on the specified molecule. Select the desired computational package from the list, and click on the right arrow to move to the next step.
Select Job OptionsFinally, you will be brought to the Job Options page. The specific options on this page will be unique to each computational package, but will include the type of job to run, theory, basis, etc. When the desired options have been set, click the right arrow to submit the job. You will now be returned to the job manager. You should see your new job listed at the bottom of the jobs list, either running or queued.
IntroductionJobs can be viewed by clicking the "View" button next to any successfully completed job listed in the job manager. You will then be brought to the View Job page, which contains the WebMO viewer, as well as a list of calculated molecular properties. The WebMO viewer contains the final optimized molecular geometry, which can be explored using the same techniques as in the editor.
Viewing Calculated PropertiesSeveral molecular properties contain an associated "View" button. Clicking this button causes the corresponding property to display on the WebMO editor. All displayed properties can be removed from the viewer by clicking the "Reset Viewer" button. In addition, the raw output of a job can be examined by clicking the "Raw Output" button.
Starting Another CalculationTo create a new job using the optimized geometry currently displayed in the WebMO viewer, simply click the "New Job Using This Geometry" button. You will then be brought to the Build Molecule page, where the geometry can be tweaked as necessary.
Exporting a MoleculeThe optimized molecular geometry can be exported in a variety of formats using the 'Export Molecule' button. Simply select the desired file format, and click the 'Export' button. You may save the resulting text file using your browsers save capabilities. To view the molecule in an external viewer (i.e., CHIME), click the 'Open in External Viewer' checkbox. job manager, you will be brought to the Import Job page.
To change your e-mail address, and e-mail notification, make the appropriate changes and click the submit button. E-mail notification will send out an e-mail to the specified address when a WebMO job is complete.