University of Alaska Fairbanks
Department of Chemistry and Biochemistry

WebMO Computational Chemistry Server Homepage

Updated 8-17-2017
 


Click graphic 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.
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.

Servers and software available at this site.

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

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. (The hyperthreading feature of the Core i7 chip doubles the number of cores visible to the operating system.) Thus WebMO will run six simultaneous 2-core jobs on Obsidian before assigning a job to the next server, Chemlinux3.  To request a machine with a particular number of threads, use the Select Server pull-down menu. 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 the user cannot tell which servers, or how many threads on a given server, are currently in use. Therefore, if you really must run a multi-core job now, first check the status of a given server by submitting a quick throw-away job to it. It that runs, kill it and submit your actual job. If the test job remains queued, kill it and test another server the same way. 

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. If you wish to compare these results with your machine, download the Gaussian 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 newest version of the software.)

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 displayed continuously in the Time column of the WebMO Job Manager. Although this value decreases considerably on completion of the job (by a factor of about 1/n where n = the number of processors), WebMO uses the 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, that is, after about 20 min of wall clock time. It can be restarted, but the best approach is to request fewer processors. This approach uses the available CPU time most efficiently. In this case, requesting 6 processors will give the minimum wall clock time (about 24 min). 



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)).


Related Topics
 

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://corsair2.cns.uaf.edu/~frank/cgi-bin/webmo/login.cgi. Enter your normal username and password, or the guest account.
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.
Molecular Graphics
View a webpage with interactive molecules: DNA, sucrose, oxycodone.
AMD's Ryzen Threadripper. AMD is now shipping the 16-core (32-thread)  Ryzen Threadripper 1950X processor. According to a benchmark test carried out by hothardware.com here, calculations are about 30% faster than Intel's 10-core (20-thread) Core i9 7900X Skylake-X processor. Both these chips retail for about $1000. The AMD part has been overclocked to 5.2 GHz with liq N2 cooling. This is obviously not practical for production servers, but indicates that substantial liquid cooling is required when all cores are running at 4 GHz or more.

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.
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.