Houk Group Computing

This is the preliminary Houk research group homepage for computing questions and answers on how to get things done. There are a number of concerns that everyone shares and sometimes work is repeated or things are done the hard way because no one knew that someone else had encountered the problem before and solved it.

Available topics/important sites:

• quiver- How to use the quiver program to calculate KIE's (pdf) from Andrew Leach
• quiver.tar- The quiver source code, executables for sgi R5K machines and linux RedHat 6.0+, and qcrunch, a program that prepares input for quiver from a formatted gaussian checkpoint file
• Gaussian and large scratch files- solving problems with running out of disk space in Gaussian
• CBS-QB3 worksheet- to do the complete basis set extrapolation procedure of Pederson without the Gaussian keyword from Bruce Hietbrink
• Swiss PDB Viewer- What is it? What can you do with it? From Christophe Alleman.
• Grasp, Molscript, and Render- a tutorial by Xiyun Zhang
• Amber- a tutorial by Yu Takano and Courtney Stanton
• Drawing IR spectra from Gaussian Frequency jobs
• Gaussian technical information including a keyword index and very useful tutorials- it's the most current manual for Gaussian essentially
• printer setup - about how to set up network printers in the group
• scripts- scripts available to the group

Getting Started

• Bruin Online page- establish new account or change password
• Information about ATS cluster. Click on "Application for an ATS Login ID" to get an account.
• Bruin dial-up- how to set up your computer at home to dial into the UCLA network. Note that all communication with the Houk machines has to go through silicon first.
• ssh- about ssh and free ssh terminal programs

Tricks of the Trade

• Convergence Problems- Changing optimization step size in Gaussian can help sometimes
  • StepSize option of Opt in Gaussian doesn't work- use
    IOP(1/8=N) where N is the stepsize (default is usually 30)