University of Alaska Fairbanks
WebMO Computational Chemistry Server Homepage
This site provides access to servers running Gaussian 09 rev D.01, MOPAC2012, and NWChem 6.1. (Please note that from time to time one or more of these computers may be temporarily off-line, and will not appear under Select Server on the Choose Computational Engine page in WebMO.) Updated 12-9-2013
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, and MOPAC. Guests may use NWChem,
and MOPAC with a cpu time limit of 60 min.
• How to log on and do a small NWChem job
• A somewhat more advanced NWChem job
• NWChem 6.1 manual (2.4 MB pdf)
• MOPAC manual online
• Tinker manual online
• Gaussian 09 Help website
• WebMO manual (3.5 MB pdf) •
Simulations in the Classroom
Gaussian Inc homepage
Chem Dept homepage.
Arctic Region Supercomputing Center (ARSC)
Online videos illustrating some aspects of running WebMO, Gaussian, and HyperChem.
|How to log on and do a
small NWChem job
If you're vaguely familiar with ab initio methods, you should be able to make this work. Otherwise, JWK can give a demo. Your computer requires no software other than a browser such as Internet Explorer with Java plug-in. Click the WebMO icon at the top-right of this page to go to WebMO.
Use the "guest" username; the password is the name of the web software mentioned at the top of this page, all lowercase. Start with the New Job tab, Create New Job. First draw a small molecule like H2O as follows: click the Build icon that looks like a small water molecule, which is the 4th one down on the left-hand toolbar. Touch the letter O on your keyboard, then left-click in the workspace. Now do Clean-Up, Comprehensive-Idealized. Click the > arrow at the bottom right. On the Choose Computation Engine page choose NWChem, Select Server, First Available, and click the > arrow. In the Calculation box, choose Optimize + Vib Freq. Submit the job by clicking the > arrow at the bottom right. The Job Manager should say Running, then after a few seconds, Complete.
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)).
The chemistry department WebMO servers are based on a Intel S5000PSL server motherboard with two 2.5 GHz quad-core Xeon processors (L5420) for a total of 8 cores. Each server has 32 GB of memory and a 1-TB hard drive. The hardware cost for one server was about $3.5K from Newegg.com.
This project is supported by grants from UAF's Technology Advisory Board in January 2009 and 2011.
Chris Iceman 907-474-6610 firstname.lastname@example.org