University of Alaska Fairbanks
Department of Chemistry and Biochemistry

WebMO Computational Chemistry Server Homepage

Contact: John Keller (jwkeller@alaska.edu) 

To log on, click on the ring.
See below for more directions.

WebMO has been updated to v. 13.1, which corrects several issues that cropped up recently regarding NWChem 6.1. Should more problems arise, please contact J. Keller or C. Iceman.  Updated 5-14-2013

This site provides access to five servers running Gaussian 09, MOPAC2012, NWChem 6.1, and Tinker 6.2.

Gaussian (http://www.gaussian.com/) is restricted to UAF students, staff, or faculty users according to the terms of UAF's license. Other Alaska users may obtain a user account for running longer NWChem, MOPAC, or Tinker jobs. Guests may use NWChem, MOPAC, and Tinker with a cpu time limit of 60 min.

NWChem (www.nwchem-sw.org) has many basic and advanced ab initio and DFT methods. See the manual link below, or visit the Pacific Northwest National Laboratory website for a complete description. The performance characteristics of NWChem and Gaussian09 are compared on Xeon and Opteron machines on the following web page.

MOPAC (http://openmopac.net) contains fast and effective semi-empirical functions (PM3, PM6 and now, PM7), but no ab initio or DFT methods. NB: to invoke the PM6 or PM7 methods, choose "Mopac," and under Theory, choose "Other", and type "PM6" or "PM7" (no quotes) in the text box.

Tinker (http://dasher.wustl.edu/ffe/) is a program from Jay Ponder's lab at Washington University that uses molecular mechanics (MM2, MM3 and others) for geometry optimization and energy calculations. It is mainly designed for protein molecular dynamics studies however the MMn methods are widely applicable to organic molecules. (WebMO cannot accept molecular dynamics jobs, only the basic MM calculations.) A molecular mechanics method is often a good choice for a rough first pass to a reasonable geometry. For example, try drawing [2,2]paracyclophane in the WebMO workspace! The WebMO Clean-Up, Comprehensive-Mechanics function does a horrible job guessing the geometry of this molecule, and Clean-Up, Mechanics, Optimize improves the situation only a little. Taking that as input, Tinker's MM3 optimization gets very close to the correct geometry in about 1 sec.

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 originally built two servers and installed WebMO and Gaussian ab initio computational chemistry software. This hardware-software combination is a good deal more powerful than HyperChem, especially in carrying out ab initio and density functional theory calculations. 

The main benefit of WebMO is the graphical user interface, which takes the user's graphical structural information and text-box entries, and constructs an input file for any computational software package that is installed. The user can check the progress of the calculation at any time, and when it is finished, the output is summarized in text and graphical formats. Here is a nice short web paper describing the features of WebMO by Will Polik and JR Schmidt, the authors and purveyors of the software.

Gaussian 09 and NWChem are also installed on the Pacman supercomputer at the Arctic Region Supercomputing Center (ARSC). Pacman has about 140 nodes, which have 1.5-to-4 times the computational capability (12, 16, or 32 cores) as measured in processor cores, compared to the 8-core servers at this site.

This WebMO installation is designed for use by any students or faculty at UAF, the State of Alaska, or beyond (within reason) for teaching or research. However, large scale computational projects should still be run at ARSC or other dedicated supercomputer centers.

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". NWChem always includes 3 whole-molecule rotations and 3 translations at the top of the table; the internal motions that we normally associate with vibrational analysis are listed starting at line 7 of that table.

A more detailed WebMO How-To webpage. This shows screen shots of setting up a NWChem optimization and frequency calculation for protonated methanethiol (CH₃SH₂⁺) using a standard ab initio method (HF/6-311++G(d,p)).