University of Alaska Fairbanks
Department of Chemistry and Biochemistry

WebMO Computational Chemistry Server Homepage

 

Go to UAF WebMO login

Click the graphic above to log in.
See below for more directions.

 Announcement. Guest users now have a 4-h cpu time limit. NWChem 6.6 is now running on two servers.
12-20-2015. You may now use your iPhone or Android device and the new WebMO app to build molecules, calculate molecular orbitals, submit jobs to servers, and view the calculation results. First, download and install the free WebMO app. The new version of this app will calculate MO's and electrostatic potential maps right on your device without having to connect to a server. The first panel shows the ESP map of formaldehyde built and calculated on an iPhone. If you wish to connect to a server, touch the "wheel" symbol at the top-right (panel 2), touch Settings (panel 3), and enter the URL of a server (panel 4). UAF's WebMO logon is http://chemlinux5.cns.uaf.edu/~frank/cgi-bin/webmo/login.cgi. Use your normal username and password to access GAUSSIAN, or the guest account to access only MOPAC and NWCHEM.

  This site provides access to servers running Gaussian 09, NWChem, 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.)

Server Cores Mem (GB) Processors Gaussian NWChem MOPAC
Chemlinux1 8 16 Xeon (2)   (6.3)
Chemlinux2 8 32 Xeon (2)  
Chemlinux3 8 32 Xeon (2)   (6.3)
Antec12 12 32 Core i7 5820K   (6.6)
Corsair2 8 24 Core i7 930   (6.6)

(10-28-2015) Antec12 was 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.

Gaussian (http://www.gaussian.com/) 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 240 min. Other UAF or Alaska users may request a no-cost user account for running longer NWChem and MOPAC jobs.

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 complete list of built-in basis sets in this version of NWChem is shown here. The "basis" section of your NWChem input file will typically show "* library cc-pvtz", where "*" refers to all atoms, "library" refers to the folder containing the files on this list, and "cc-pvtz" is one line as it appears in the list. Descriptions, literature references, and downloadable files for 540 basis sets are available at the PNNL Basis Set Exchange website.

If you require your own local installation of NWChem, here is a text file describing how to compile and install NWchem on plain vanilla Linux systems like these, i.e. ones without a commercial math package. 

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 PM7, choose "Mopac," and under Theory, choose "Other", and enter "PM7" (no quotes) in the text box.                                                    

 Useful Links
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)

Introduction
WebMO is a java-based web front-end for ab initio computational chemistry software. 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 short article describing the features of WebMO by Will Polik and J.R. Schmidt, the authors and purveyors of the software.

Simulations in the Classroom
See an article about the use of WebMO in University of Wisconsin-Madison classrooms. J.R. Schmidt is featured.


Web links
WebMO homepage.
Gaussian Inc homepage 
NWChem homepage
Chem Dept homepage
Arctic Region Supercomputing Center
UAF  
Online videos illustrating some aspects of running WebMO, Gaussian, and HyperChem. including links to 3 YouTube videos featuring HyperChem ("Building Morphine", "Automated Conformation Search", "Optimizing a Transition State".)
"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 Firefox or Internet Explorer with the latest Java plug-in (Chrome and Edge do not support Java). 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 the "Reset Viewer" button at the bottom of the molecule workspace. 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  start at line 7.

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)).

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.
Hardware
The original chemistry department WebMO servers (chemlinuxn) 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. A current quad- or hexa-core Intel consumer processor can match or beat our dual-Xeon format.
Grant Support
This project is supported by grants from UAF's Technology Advisory Board in January 2009 and 2011.
Contact
John Keller 907-888-7278 jwkeller at alaska.edu