Tutorial

Download the PDF version of this tutorial here.

Note: Click on any thumbnail below for full size image.

WebMO Portal

• The WebMO portal allows users easy access to computational chemistry applications through a web page interface. New and experienced users can take advantage for the custom computational engines that provide well defined application parameters and convenient menus. WebMO is integrated with the large Dell cluster U2 and several departmental clusters.
• WebMO provides access to popular applications such as GAMESS, GAUSSIAN, NWCHEM and Q-Chem.
  • WebMO Applications and Queues
• Features of WebMO:
  • Create and upload input modules.
  • Submit the calculation to one of the computational clusters.
    • Jobs run under the account of the user.
  • View output
  • Manage jobs and data files.

Required Software

• The WebMO interface is requires a web browser and Java Runtime Environment on your workstation.
• Browsers that appear to work well:
  • MAC OSX
    • Firefox 2.0.0.11 and Java (JRE) 1.4.2 or greater
    • Safari 2.0.4 or greater and Java (JRE) 1.4.2 or greater
  • RedHat Enterprise Linux 4
    • Firefox 2.0.0.11 and Java (JRE) 1.6.0 or greater
  • Ubuntu 6.0.6
    • Firefox 1.5.0.12 or greater and Java (JRE) 1.4.2 or greater
  • Windows XP Professional (Service Pack 2)
    • Internet Explorer 7 and Java (JRE) 1.6.0 or greater
    • Firefox 2.0.0.7 and Java 1.6.0 or greater

• The latest browser support information from WebMO.

Accessing the WebMO Portal

• The CCR WebMO web page provides a brief introduction and link to the login WebMO.
• A login account to the WebMO portal is required.
• Access to WebMO must be enabled, even for users that have a CCR account.
• UB faculty interested in using WebMO should contact the CCR staff for an account.
• Connecting to the WebMO Portal (either of 3 ways):
  1. URL: https://webmo.ccr.buffalo.edu/~webmo/cgi-bin/login.cgi
  2. Click here: WebMO
  3. Through the CCR website:
     • http://www.ccr.buffalo.edu
     • Click on User Info tab
     • Select Web Portals
     • Click on WebMO
     • Click on WebMO Web Portal

Certificate Issues

• The first login to WebMO requires acceptance of the SSL certificate. This is browser dependent.
  • WebMO Certificate Information

Login to WebMO

• The username is your UBIT username.
  • The password is the same on the U2 cluster.
• Enter UBIT username and U2 password.

Job Manager

• The Job Manager is the first window presented when logging into WebMO.

• This interface allows the user to create and submit jobs, as well as manage jobs and data files.
• Tabs:
  • New Job - create and submit jobs
  • Refresh - queries the WebMO server for updated job status
  • Download - save data files to workstation
  • Move To - relocate the data files of a job to another folder
  • Delete - delete the folder of a job, which contains the input and output files
  • Utils - help information and change email address
    • Note: password cannot be changed in WebMO, instead login to U2
  • Logout - logout from the WebMO interface
• Manage Folders allows users to create folders

Creating a Job

• A molecule can be built or uploaded in the Job Manager

Building a Molecule

• Click New Job tab in the Job Manager Window
  • Click on Create New Job

• Click on Open Editor in Build Molecule window

• Click on Build
  • Select atom, then click in window

• Create bonds
  • Click on atom, then move mouse to another atom

• Cleanup geometry
  • Click on Clean-Up
  • Select Geometry

• Built water module
• Click on File
  • Select close
• Click on Right Arrow in Build Molecule window to continue

• More information on building a molecule, including adjusting a dihedral angle.
  • WebMO Building a Molecule

Loading a PDB file

• Click New Job tab in the Job Manager Window
  • Click on Import Molecule

• Click on Format
  • Select PDB from pull-down format menu

• Check on Generate Bonds
• Click on Browse (option 1)
  • Locate the PDB file on your workstation
  • Click on Import

• Imported water molecule
• Click on Right Arrow in Build Molecule window to continue

Running a Job

Choose Computational Engine

• Several applications and job queues are listed.
  • WebMO Applications and Queues
  • The route-u2 is available to all CCR users.

• Select the application GAMESS and the route-u2
  • Click on Right Arrow to proceed

Configure GAMESS Job Options

• Each application has custom input options.

Job Options Tab

• Custom options:
  • job name
  • type of calculation
  • molecular theory
    • DFT functional for the DFT theory
  • basis set
  • charge
  • multiplicity

• Select Geometry Optimization in the Calculation menu

enter image for job options window

Advanced Tab

• Additional calculation parameters
• Number of nodes (machines) and processors (cpus per machine)
  • default values are shown
• Some applications allow parallel processing
  • If in doubt about problem scaling, then use the default values

Preview Tab

• Allows users to view and modify the input file
  • Click on Generate

Submit Job

• Click Right Arrow on any tab

• Click Okay to continue

• Once job has been submitted, the user is returned to the Job Manager window

Analysis of Job Output

• The Job Manager window updates when job status changes

• Click on the magnifying glass in the Action Column for the job
  • Output of job is displayed in a new window

• Actions - left side of window
  • View output text file
  • All files displays all input and output files of the job

• This output includes a visualization of the optimization and a graph of geometry sequence energies.

• Molecular Orbital Visualizations:
  • Open with Java Web Start Launcher