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. The Northwest Regional Meeting of the American Chemical Society NORM2016 will be held June 26-29 in Anchorage. A Computational Chemistry Symposium will be presented on Tuesday, June 28 and Wednesday, June 29. Check out the details here. The conference website is here NORM2016 .

Also of interest is a workshop for chemistry instructors and students on "Web-Based Molecular Modeling." For more information, click here.

Need to run an NBO (Natural Bond Orbital) calculation using the built-in NBO capability of Gaussian? At this site, Gaussian is available only to UAF users, as stipulated by our Gaussian license. Alternatively, the WebMO Demo site here can run small Gaussian jobs. That server has limitations, but it should be sufficient to run a Gaussian Natural Bond Orbitals job on a molecule containing up to about 8 heavy atoms.
 Guest users now have a 4-h cpu time limit. See further discussion below on how to best use this time. UAF or other Alaska educational users who wish to run jobs longer than 4-h should contact John Keller to obtain a no-cost user account.
WebMO requires a browser with the Java Runtime Environment installed. These can be for Windows, Firefox and Internet Explorer; for OS X, Safari; and for Linux, Firefox. The most recent JRE is version 8 update 91 as of 6-7-2016. Note that Chrome, Edge, or Opera browsers do not support Java.

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.


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 MOPAC2016.

Server Cores Processors Mem (GB) Processors Gaussian NWChem MOPAC
Chemlinux1 8 8 16 Xeon (2)   (6.3)
Chemlinux2 8 8 32 Xeon (2)    (6.6)
Chemlinux3 8 8 32 Xeon (2)   (6.3)
Antec12 6 12 32 Core i7 5820K   (6.6)
Corsair2 4 8 24 Core i7 930   (6.6)

(10-28-2015) Antec12 was rebuilt with a 6-core Intel processor (or 12 effective processors due to the hyperthreading capability of this processor). In one recent test of servers chemlinux1-3, antec12,and corsair2, 1-chloro-2-phenylbenzene was optimized at the B3LYP/6-31+G** level of theory using Gaussian 09, starting with a nearly planar conformation with the results shown below. The same optimization task using NWChem (8 processors) required 2 h 48 m, 2 h 23 m, 2 h 32 m, 1 h 24 m, and 2 h 45 m.

The above Gaussian 09 optimization required 19 minutes on Obsidian, a newer 6-core, 32-GB Core i7 5930K machine with a solid state drive; and 22 minutes on a 16-core, 64-GB node in the Pacman cluster at ARSC.

Gaussian (http://www.gaussian.com/) is restricted to UAF students, staff, or faculty users according to the terms of UAF's Gaussian license.

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. Descriptions, literature references, and downloadable files for 540 basis sets in NWChem, Gaussian, and other formats are available at the PNNL Basis Set Exchange website.

NWChem: Dealing with the 4-h CPU limit of the guest account. During an NWChem calculation the current value of elapsed CPU time is recorded continuously in the Time column of the WebMO Job Manager. Although this value decreases considerably on completion of the job (by a factor of 1/n where n = the number of processors), WebMO uses the original displayed elapsed time to limit the CPU time of the guest account. The problem is that multi-processor jobs are inefficient, in NWChem at least. For example, if a guest requests all 12 multi-threaded processors of Antec12 for a large job, the 4-h limit will be reached after about 20 min of wall clock time, which causes WebMO to terminate the calculation. It can be restarted, but a better approach is to request fewer processors, since this is more efficient use of CPU time. A random example is optimization of the water hexamer. Using only 4 processors, the 48-cycle optimization is complete in 25 min of wall clock time. If 12 processors are requested, the job terminates after 20 min having completed only 38 cycles!



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)
Web links
WebMO
Gaussian  
NWChem 
UAF Chem Dept 
Arctic Region Supercomputing Center
UAF  
NEW YouTube videos available showing topics related to WebMO, Gaussian, NWChem and HyperChem.
"Chemistry Graphics" website showing how to use WebMO, Jmol 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