University of Alaska Fairbanks
Department of Chemistry and Biochemistry

WebMO Computational Chemistry Server Homepage

Updated 11-8-2016



Click the molecule to log in.
See below for more directions.

OpenSSL. 11-11-2016. 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 in a week or so.
You are responsible for backing up your output files. Select the important jobs, then use the "Download" menu to download an archive and a spreadsheet. The spreadsheet summarizes the contents of the selected jobs, which will help you navigate the files off-line. Gaussian users: it is easier to find your data if you name each job in a rational way, such as molecule-basis-method-jobtype. For example Benzene-ccpVTZ-m062x-OptFreq. Also, save a checkpoint file for each job and name it the same way: Benzene-ccpVTZ-m062x-OptFreq.chk. The WebMO archive contains only folders with job number labels, therefore, other than opening up the actual files, this is the only way to determine what type of job is within the folder. You could also check the spreadsheet if you saved it.
Off-line analysis of Gaussian output files (.log and .fchk). These files can be opened by Jmol, GaussView, and other programs.

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.

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.
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. As an example, the first panel on the left shows the electrostatic potental 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 https://chemlinux5.cns.uaf.edu/~frank/cgi-bin/webmo/login.cgi. Enter your normal username and password, or the guest account.

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)   
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)

Benchmarking UAF chemistry servers. In one recent test, 1-chloro-2-phenylbenzene was optimized at the B3LYP/6-31+G** level of theory using Gaussian 09, starting with a nearly planar conformation (first six results in the chart below). The optimization was also carried out on a 16-core node in the Pacman cluster at RCS, and on a Core i7 5930K machine (Obsidian) with a solid state drive (last two results in the chart below). If you wish to compare these results with your favorite quantum package and machine, download the input file for this test here.

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.                                                     

 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
Web links
 WebMO
Gaussian  
 NWChem 
UAF Chem Dept 
Research Computing Systems (RCS, formerly Arctic Region Supercomputing Center)
UAF  
YouTube videos 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
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)).

 
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 the 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