WebMO Tour

	Recent news WebMO 13.1 is now available for free download! WebMO 13.1 Pro and Enterprise have a variety of additional features and is available for purchase. WebMO can now build bulk, periodic (1D, 2D, 3D) materials. Periodic calculations are supported in Gaussian, PWSCF, and VASP!
June 20, 2013

WebMO Tour

The following sections will take you through a brief tour of the various components of WebMO. Each of the following sections highlights a particular aspect of WebMO system, from job setup to the viewing of results.

WebMO Editor

The WebMO editor is a true 3D molecular editor. The editor is used to specify the molecular geometry to be used for computation. The editor features an easy use, click-and-draw interface, true 3D rotation, translation, and zooming, as well as the ability to display and/or adjust bond distances, angles, and dihedral angles. Building moderate to large molecules is easy with the editor's built-in fragment library and the ability to translate, rotate, duplicate, and delete selected portions of a molecule.

Before a structure is submitted, the editor's clean-up feautures can be utilized to automatically add hydrogens, set hybridization, idealize bond angles and bond lengths. These clean-up features lead to a reasonable starting geometry for further calculations.

Choose Computational Engine

Before selecting job options, the user must specify the computational engine to be used in the calculation. WebMO supports a variety of computational engines, including Gaussian 94/98, MOPAC 6/7/2000, and GAMESS. These computational engines can be enabled, disabled, and configured using the on-line WebMO administration.

Job Options

WebMO offers a wide variety of jobs options which are used to specify the calculation, level of theory, and basis set for a particular calculation. WebMO offers reasonable suggestions for the novice, yet provides enough flexability for computational chemistry research. WebMO achieves this combination by providing a large set of built in options, while always providing a mechanism for specifying an unlisted option.

WebMO features a fully customizable set of job calculation templates for each computational engine. These templates allow WebMO to be easily extended to support any type of calculation that is desired by editing a simple text file. The template system includes powerful conditional statements that further enhance the flexibility of the job calculation template system. The default WebMO templates include support for single point energy, geometry optimization, transition state optimization, vibrational frequencies, NMR shifts, bond order analysis, and MO calculations.

Preview Input File

In order to provide the user with to absolute greatest possible control, the job options page contains an option to preview the Gaussian input file. When this option is selected, the user is given an opportunity to edit the Gaussian input file before it is submitted to Gaussian for computation. By editing the input file, additional options such as coordinate scanning or chemical isotopes can be specified.

Results Visualization

WebMO offers a wide range of features that make it easy to visualize the results of your computation. The WebMO result visualization package incoperates a 3D viewer with the ability to rotate, translate, and zoom. Properties such as vibrational modes, partial charges, and dipole moment can be overlayed on the molecule to allow for easy visualization.

IR and NMR spectra can be visualized using the WebMO spectrum viewer.

The WebMO results summary also includes tables of energies, rotational constants, partial charges, bond orders, vibrational frequencies, and NMR shifts. Of course, the user is always provided with direct access to the raw, text output from the computational chemistry software used for the calculation. Thus, it is trivial to access any additional properties of interest that are not automatically parsed by WebMO.

Using a separate Java application, WebMO Pro allows the visualization of molecular orbitals. Simply click on the associated "View" button next to the desired MO on the "View Results" page, and the orbital automatically opens in the MOViewer application. The following are examples of the output of MOViewer:


Ethane HOMO	Ethane LUMO

Job Manager

The WebMO job manager is the central location from which all WebMO processes are control. From the job manager, WebMO jobs can be started, monitored, killed, viewed, imported, downloaded or deleted. It also provides vital statistics about the number of currenty queued WebMO jobs and any cpu time limits that have been imposed. The most prominent item in the job manager is a list of jobs, including those currently running as well as those previously run. The options associated with each job depend on the jobs status; for example, completed jobs may be viewed, downloaded, or deleted. In contrast, while running jobs may viewed or killed, they cannot be downloaded.