University of Alaska Fairbanks
Department of Chemistry and Biochemistry

WebMO Computational Chemistry Server Homepage

Updated 2-11-2017
 


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.
The annual popularity poll for density functionals: edition 2016

The results are in. The top 3 remain the same as the past five years, while at the same time ωB97X-D and B3LYP-D consolidate their 4th and 5th position. The number of participants has increased 30% (99), but the total number of responses for part three with eleven properties (reaction barriers; normal mode analysis; chiroptical properties; hydrogen bonds; excitation energies; main group elements; transition metals; relativistic elements; NMR shieldings/couplings; geometries; spin-state splittings) has decreased slightly.  PDF

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 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) 
Corsair3 10 20 64 Core i7 9650X  

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 was Obsidian, a Core i7 5930K machine with a 1-TB Samsung 850 EVO solid state drive. The speed of Corsair3 is due to its greater number of cores, its 1-TB Samsung 960 EVO M.2 solid state drive, and the fact that it is overclocked to 4.1 GHz using gaming settings on the MSI X99A Gaming Pro Carbon motherboard. The maximum temperature of the Core i7 9650X processor is kept below 74 C with a water cooler (Corsair H100i V2). If you wish to compare these results with your favorite quantum package and machine, download the input file here.

Gaussian (http://www.gaussian.com/) 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 (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 10 or 12 multi-threaded processors of Antec12 are requested for the large job shown below, the 4-h limit is reached after about 20 min of wall clock time, and WebMO therefore terminates the calculation. It can be restarted, but a better approach is to request fewer processors, which makes more efficient use of the available CPU time. 



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
More Useful Web links
 WebMO inc. homepage
Gaussian software  
 NWChem software 
UAF Chem Dept 
Research Computing Systems (RCS, formerly Arctic Region Supercomputing Center)
UAF  
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)).

 
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. 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.
Contact
John Keller 907-888-7278 jwkeller at alaska.edu
 
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The UAF Dept of Chemistry and Biochemistry serves Alaska and the Nation through research and scholarship in chemistry, and in the environmental and biomedical sciences.

For questions or comments regarding this website, contact jwkeller@alaska.edu or chemistry.uaf@alaska.edu.