University of Alaska Fairbanks
WebMO Computational Chemistry Server Homepage
Contact: John Keller (email@example.com)
WebMO has been updated to v. 13.1, which corrects several issues that cropped up recently regarding NWChem 6.1. Should more problems arise, please contact J. Keller or C. Iceman. Updated 5-14-2013
This site provides access to five servers running Gaussian 09, MOPAC2012, NWChem 6.1, and Tinker 6.2.
is restricted to UAF students, staff, or faculty users according to the terms of UAF's
license. Other Alaska users may obtain a
user account for running longer NWChem, MOPAC, or Tinker jobs. Guests may use
NWChem, MOPAC, and Tinker with a cpu time limit of 60 min.
Tinker (http://dasher.wustl.edu/ffe/) is a program from Jay Ponder's lab at Washington University that uses molecular mechanics (MM2, MM3 and others) for geometry optimization and energy calculations. It is mainly designed for protein molecular dynamics studies however the MMn methods are widely applicable to organic molecules. (WebMO cannot accept molecular dynamics jobs, only the basic MM calculations.) A molecular mechanics method is often a good choice for a rough first pass to a reasonable geometry. For example, try drawing [2,2]paracyclophane in the WebMO workspace! The WebMO Clean-Up, Comprehensive-Mechanics function does a horrible job guessing the geometry of this molecule, and Clean-Up, Mechanics, Optimize improves the situation only a little. Taking that as input, Tinker's MM3 optimization gets very close to the correct geometry in about 1 sec.
• How to
log on and do a small NWChem job
• A somewhat more advanced NWChem job
• NWChem 6.1 manual (2.4 MB pdf)
• MOPAC manual online
• Tinker manual online
• Gaussian 09 Help website
• WebMO manual (3.5 MB pdf)
Chemistry graphics How-To using
the WebMO interface, Jmol, MarvinSketch and other free Windows and
• These pages show examples and videos of how to prepare formulas, and static or rotatable 3D images of molecules and molecular orbitals.
|2011-12 utilization of UAF WebMO servers. So far during this academic year, about 1100 jobs have been submitted to our servers, mainly from students in Inorganic Chemistry 202, Physical Chemistry 332, and by students and faculty carrying out research projects. Calculations have involved, among others, optimization and vibrational analysis of transition metal complexes, cyclodextrins, and sulfur dioxide complexes. The system had a 99.99% uptime performance this year. During the past three years 7000+ jobs have been submitted.|
The main benefit of WebMO is the graphical user interface, which 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. Here is a nice short web paper describing the features of WebMO by Will Polik and JR Schmidt, the authors and purveyors of the software.
Gaussian 09 and NWChem are also installed on the Pacman supercomputer at the Arctic Region Supercomputing Center (ARSC). Pacman has about 140 nodes, which have 1.5-to-4 times the computational capability (12, 16, or 32 cores) as measured in processor cores, compared to the 8-core servers at this site.
This WebMO installation is designed for use by any students or faculty at UAF, the State of Alaska, or beyond (within reason) for teaching or research. However, large scale computational projects should still be run at ARSC or other dedicated supercomputer centers.
Gaussian Inc homepage
Chem Dept homepage.
Arctic Region Supercomputing Center (ARSC)
Online videos illustrating some aspects of running WebMO, Gaussian, and HyperChem.
|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 Internet Explorer with Java plug-in. 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 "Reset Viewer". 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 are listed starting at line 7 of that table.
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)).
|Ab Initio Software
The computational software is Gaussian 09 or NWChem 6.1. These have many ab initio, density functional theory, correlated methods such as MP2, and other more advanced methods. Gaussian is the standard ab initio package used by most computational chemists world-wide.
The chemistry department WebMO servers 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. The hardware cost for one server was about $3.5K from Newegg.com. The 16-core node is a SunFire x4600 M2 with eight dual-core Opteron processors and four 72-GB 10K SAS drives in RAID0.
This project is supported by grants from UAF's Technology Advisory Board in January 2009 and 2011.
John Keller 907-888-7278 or firstname.lastname@example.org If JK is not available to answer the question, consult a textbook on computational chemistry, visit the FAQ pages of NWChem, http://www.emsl.pnl.gov/docs/nwchem/support/faq/NWChem_FAQ.html , see the Gaussian manual, or go to a computational chemistry discussion board.
This system should still be considered in testing mode. It may suffer unannounced outages, including hard disk failure or network glitches, which could prevent you from connecting to the server. Save any valuable research or class output on your local media using the Download Job Archive button in WebMO. Should there be a temporary outage, your Gaussian output files (.log) can be opened and analyzed using GaussView software which is available on Chemistry Dept computers, or with other downloadable freeware, or even at the main WebMO website in Michigan. Or, download the jobs in HTML format, and you can open them locally with any web browser.
|2011 Gaussian Workshop.
Click here to
view a webpage with links to (1) the PDF version of the 12-13-11 workshop
PowerPoint slides, (2) videos showing various operations
covered in the workshop, and (3) text entries that may be useful for
2012 WebMO-Q-Chem Workshop. Click here for a video/audio version (120 MB pdf)