University of Alaska Fairbanks
Department of Chemistry and Biochemistry

WebMO Computational Chemistry Server Homepage

Go directly to the UAF WebMO login

Updated 9-7-09 by JK

Introduction
WebMO is a java-based web front-end for ab initio computational chemistry software. With funding from the UAF Technology Advisory Board, John Keller of this department built two servers and installed Gaussian 03 ab initio computational chemistry software. This hardware-software combination is a good deal more powerful in terms of speed and versatility than HyperChem. HyperChem has its place as a relatively easy to use (yes!) tool for learning the basics of computational molecular modeling, however it is severely limited in the area of ab initio and density functional theory calculations. The latter are generally more accurate, albeit slower, than molecular mechanics or semi-empirical methods.

The Gaussian 03 program as well as other packages such as NWChem are also installed on the Midnight supercomputer at the Arctic Region Supercomputing Center (ARSC). Midnight has about 400 nodes, each of which is about the same computational capability as one server here. What this WebMO installation offers is ease of access, and a graphical interface for input and output to Gaussian. The ARSC computers have a complicated - and effective - security access system.

This WebMO installation is designed for use by any UAF students or faculty, within reason, for teaching or research. Large scale computational projects should still be run at ARSC. The new chemistry course Molecular Modeling Chem 623 which will be offered spring semester 2010 will use the WebMO servers, HyperChem, and probably ARSC computers.

To see the results, click the magnifying glass icon. To animate a vibration, click the "animate" icon of whichever vibration you wish to see in the Vibrational Modes table (near the bottom of the Calculated Quantities box). To stop the animation, click "Reset Viewer".

The time limit on the guest account is 5.0 min. You can actually do a pretty good calculation in 5 min with these computers. For example, geometry optimization and frequency calculation on propanoic acid using an accurate method (HF/6-311+G**) with 4 processors takes 4.5 min starting with the molecular mechanics-optimized geometry. This would take at least 2 hours with HyperChem on a PC. This speedup is due to the more efficient computational algorithms in Gaussian, and enhanced compute hardware. In particular, HyperChem cannot utilize multiple processors.

To do jobs longer than 5-min, or more than a few test jobs, see JK for a username and password. This is better than using the guest account, because it will save your jobs under your account name.

See a more detailed WebMO How-To webpage by following this link. This shows screen shots of setting up an optimization and frequency calculation for methanethiol using the B3LYP/6-311+G* level of theory.
 

WebMO can in theory manage several different programs such as NWChem, GAMESS, Q-Chem, Molpro, the protein modeling system Tinker, and others. Several of these are free downloads, and they may be installed in the future.

The OS is 64-bit openSUSE 11.1, which is free.