University of Alaska Fairbanks
WebMO Computational Chemistry Server Homepage
|WebMO requires a browser with Java (the Java Runtime Environment, or JRE) installed. For Windows, these are Firefox and Internet Explorer; for OS X, Safari and Firefox; and for Linux, Firefox. The Chrome, Edge, and Opera browsers do not support Java. As of 7-19-2016, the most recent version of Java is v 8, update 101.|
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. Near the bottom of the Build Molecule window you will see a "Lookup Molecule" button. Click that and enter its common or IUPAC name. For example (to check your aldohexose naming skills) enter L-gulose.
|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 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.|
Simulations in the Classroom
|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.
(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.
is restricted to UAF students, staff, or faculty users according to the terms of UAF's
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!
• 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) •
• UAF Chem Dept
• Arctic Region Supercomputing Center
• 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.|
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.
This project is supported by grants from UAF's Technology Advisory Board in January 2009 and 2011.
John Keller 907-888-7278 jwkeller at alaska.edu