University of Alaska Fairbanks
Department of Chemistry and Biochemistry

WebMO Computational Chemistry Server Homepage

Updated 5-30-2017

Click the molecule to log in.
See below for more directions.
WebMO is a browser based GUI for ab initio computational chemistry software. WebMO 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. For more details, visit the WebMO website.

Chemistry Seminar Web Links - Feb. 9, 2017

OpenSSL. Your connections to the WebMO website are now encrypted by the Linux openSSL package, which  adds a certain level of security to this site. Clicking the above graphic will now take you to https://chemlinux... .  You should see a green padlock icon on the address bar. If you bookmark the login page, please change the address to https://..  now. The old address will be turned off at some point.
WebMO Tip: Lookup Molecule. WebMO can search several databases for the 3D structure of a named molecule. Log on and click New Job, Create New Job. Click the main menu item Lookup. Enter a common or IUPAC name, and click OK.
NBO (Natural Bond Orbital) calculations using the WebMO demo site. Gaussian contains a built-in NBO 3.0 capability, but Gaussian is available only to UAF users at this site, as stipulated by our license. However, the WebMO demo site here will run free Gaussian jobs for up to 60 seconds. It should be able to do an NBO job on a small-ish molecule (about 8 or less heavy atoms) within this time limit.
Intel announces 16- and 18-core (32- and 36-thread) Core i9 processors. See the article in the online PC Magazine. It looks like wall-clock times for DFT optimization and frequency jobs will continue to decrease, given the excellent parallel performance of Gaussian and MOPAC. These chips and the necessary motherboards will be available sometime in late 2017 or early 2018.
Guest users 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.

You may use your iPhone or Android device and the WebMO app to build molecules, calculate molecular orbitals, submit jobs to servers, and view the calculation results. If you wish to connect to a server, touch the "wheel" symbol at the top-right in the app, touch Settings, and enter the URL of a server. UAF's WebMO logon is Enter your normal username and password, or the guest account.

Servers and software available at this site.

Server Cores Threads Memory (GB) Processors Gaussian NWChem MOPAC
Chemlinux3 8 8 16 Xeon (2)   (6.3)
Chemlinux1 8 8 32 Xeon (2)    (6.3) 
Chemlinux2 8 8 32 Xeon (2)  
Antec12 6 12 32 Core i7 5820K   (6.6)
Corsair3 10 20 64 Core i7 9650X     (6.6) 
Obsidian 6 12 32 Core i7 5930K    (6.6) 
Corsair2 4 8 24 Core i7 930    (6.6) 

In the table above, servers are listed in the "First Available" order. If you do not specify a server under the Select Server box of WebMO, your job is assigned in this order starting at the top of the list. Generally the default number of cores, i.e. threads, assigned per job is 2, unless you specify more on the Advanced tab. Thus WebMO will run four simultaneous 2-core jobs on Chemlinux3 before assigning a job to the next server, which is Chemlinux1. The hyperthreading feature of Core i7 chips doubles the number of "cores" visible to the operating system. To request a Core i7 machine, use the Select Server pull-down menu. Then under the Advanced tab set the number of cores, i.e. threads, to be equal to or less than the number in column 3.
     A limitation of the WebMO job queuing system is that users cannot tell which servers are currently in use. Therefore, if you really must run a multi-core job now, first check the status of Corsair3 by submitting a quick throw-away job to it. It that runs, kill it and submit your big job. If that job remains queued, test the next fastest server, Obsidian, the same way. If Obsidian is in fact available, it may be faster to run your job there, rather than wait for Corsair3 to become available.

Benchmarking UAF chemistry servers. As a comparison of computing speed, 1-chloro-2-phenylbenzene was optimized on each server using Gaussian 09 with the B3LYP/6-31+G(d,p) model chemistry. Also tested were Obsidian, a Core i7 5930K machine with a 1-TB Samsung 850 EVO solid state drive, and Corsair3 with a 1-TB Samsung 960 EVO M.2 solid state drive. Corair3 is overclocked to 4.1 GHz; the processor temperatures are kept below 74 C with a Corsair H100i V2 water cooler. If you wish to compare these results with your machine, download the Gaussian input file here.

Gaussian ( is restricted to UAF students, staff, or faculty users according to the terms of UAF's Gaussian license. New. Help files for Gaussian09 may be accessed here. (The Gaussian website now links only to the help files for Gaussian16, the new version of the software available in January 2017.)

NWChem ( 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 10 or 12 multi-threaded processors are requested for the water hexamer optimization shown below, the 4-h limit is reached before the calculation can be completed - after about 20 min of wall clock time. It can be restarted, but the best approach is to request fewer processors, which makes more efficient use of the available CPU time. Requesting 6 processors will give the minimum wall clock time under these conditions. 

MOPAC ( contains fast and effective semi-empirical functions (PM3, PM6 and now, PM7), but no ab initio or DFT methods.                                                     

NEW Installing the parallel version of NWChem on CentOS 7.2 A how-to article is available for download here. Click here to obtain a zipped folder containing the required .patch files and several .sh script files, as explained in the how-to article.
Useful Links
WebMO online comprehensive help
How to log on to this WebMO site as Guest, and do a small NWChem job
A more advanced NWChem job
MOPAC manual online
Gaussian 09 Help website
More Useful Web links
 WebMO inc. homepage
Gaussian software  
 NWChem software 
UAF Chem Dept 
Research Computing Systems (RCS, formerly Arctic Region Supercomputing Center)
Videos and PDFs on 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
Only a browser (Chrome, Firefox, or other) is required. Click the WebMO icon at the top-right of this page to go to the logon page. Login with "guest" username;  the passwrd is webmo.

Click the New Job tab, Create New Job. Draw a small molecule like H2O as follows: click the red Build icon that looks like a water molecule, which is topmost 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;  leave the default Hartree-Fock (HF) theory, 6-31G(d) basis set, 0 charge, and Singlet multiplicity.  Submit the job by clicking the > arrow at the bottom right. The Job Manager should first say Queued, then 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. 

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 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. Current hexa- and deca-core Intel processors match or beat the dual-Xeon format.
Grant Support
This project is supported by grants from UAF's Technology Advisory Board in January 2009 and 2011.
John Keller 907-888-7278 jwkeller at
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