University of Alaska Fairbanks
WebMO Computational Chemistry Server Homepage
|Announcement. Guest users now have a 3-h cpu time limit. NWChem 6.6 is now running on two servers.|
|NWChem with Python. This installation now includes the Python scripting function, which is necessary for coordinate scanning. WebMO includes a "Coordinate Scan" option under Calculation: click the Preview tab and the Generate button to view the editable NWChem input file. The terms in the Python script section must be entered manually. For clues on how to set this section, go to the NWChem website (www.nwchem-sw.org), click the Documentation link near the top of the page, click "Controlling NWChem with Python" at the bottom of the outline.|
|You may now use your iPhone or iPad and the new WebMO app to build molecules, submit jobs to this server site, and view the calculation results. First, download and install the WebMO app ($4.99).|
|A settings entry for WebMO is installed along with the main app icon. Go to Settings, WebMO, and enter the URL of this server's login page. You can find this by clicking the graphic at the top right, the copying the URL that appears in your browser's address box. Also enter your username and password, or "guest" and the password described below.||
The app works almost the same way as Java pages accessed with
a computer browser: Draw a molecule with your fingertip. Choose the WebMO
icon at the bottom right to begin the process of submitting a job.
This image is a p-MO of the thioformate ion calculated with MOPAC2012.
This site provides access to servers running Gaussian 09 rev D.01, NWChem 6.3, and MOPAC2012. (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.)
(10-28-2015) Antec12 was recently rebuilt with a 6-core Intel processor (note that the hyperthreading capability of this processor lets the OS see twice as many effective cores). In one recent test, 1-chloro-2-phenylbenzene was optimized at the B3LYP/6-31G* level of theory using Gaussian 09, starting with the planar conformation. The job was repeated on all four servers using the maximum number of processors; it required 11 steps on each, and respectively, 7, 7, 7 and 4 minutes of wall clock time. Vibrational frequency jobs on the optimized structure at the same level of theory required respectively, 5, 4, 4, and 3 minutes.
is restricted to UAF students, staff, or faculty users according to the terms of UAF's
Gaussian license. Guests may use NWChem
and MOPAC with a cpu time limit of 180 min.
Other UAF or Alaska users may request a no-cost user account for
running longer NWChem and MOPAC jobs.
If you require your own local installation of NWChem, here is a text
compile and install NWchem on plain vanilla Linux systems like
these, i.e. ones without a commercial math package.
• How to log on and do a small NWChem job
• A somewhat more advanced NWChem job
• MOPAC manual online
• Gaussian 09 Help website
• WebMO manual (3.5 MB pdf) •
Gaussian Inc homepage
Chem Dept homepage.
Arctic Region Supercomputing Center
NEW! Online videos illustrating some aspects of running WebMO, Gaussian, and HyperChem. including links to 3 YouTube videos featuring HyperChem ("Building Morphine", "Automated Conformation Search", and "Optimizing a Transition State".
NEW! "Chemistry Graphics" website showing how to use WebMO and other applications to prepare seminar slides
|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.
John Keller 907-888-7278 jwkeller at alaska.edu