Tutorials

This page contains some tutorials that I started while a postdoc at Stanford University. We'd also like to bring you some new tutorials about how to run TeraChem shortly. In the meantime, I'll be posting some elective slides that cover the basics of force fields and electronic structure (density functional theory, wave function theory....). Please let us know what you think (the 'fun' link in the menubar above)!

Reader's Choice: X-ray absorption spectroscopy
Tuesday, September 4, 2012
Our next reader’s choice topic is to review simulating K-edge X-ray absorption spectra with Quantum-ESPRESSO.  Thanks to everyone who voted for which topic they’d like to see covered.  I’d like to encourage you to keep voting, and if you don’t see your preferred topic in the list, you can always... (read more)
Reader's Choice: DFT+U
Tuesday, August 7, 2012
Thanks to everyone who voted for which topic they’d like to see covered next. It was a close one, but the first subject to hit the minimum threshold was DFT+U. I’d like to encourage you to keep voting - the next topic that has the highest votes next month will be the focus of the September tutorial... (read more)
Summer Hiatus
Tuesday, July 10, 2012
The tutorials will be going up less frequently over the summer. These tutorials have been online for about a year now. So, it’s a great time to get input from you about what you’d like to see more of and also to take a look back at some of the topics covered.   What would you like to see next? I... (read more)
Quick-tip: Building molecules with Molden
Tuesday, June 12, 2012
When starting a project, one of the first things we need to do is to build up the system we wish to study. This can be really easy if studying a system with available experimental coordinates or a previous paper.  Additionally, simple solid state materials often only require that you know the... (read more)
Quickstart with xmgrace
Tuesday, May 15, 2012
There are a lot of tools you can use to graph your data.  For graphing curves, I think xmgrace is one of the most versatile tools.  Today I’ll go over some handy tips and tricks I’ve learned with xmgrace.  If you use a mac, you may want to download a binary that you can get access to at the bottom... (read more)
Convergence 101
Tuesday, April 17, 2012
When starting any new series of simulations with Quantum-ESPRESSO or any other code, the first thing we need to do is to choose our run parameters.  While an experienced computational researcher will have general rules of thumb for what cutoffs or cell sizes to use and how many k-points, it can... (read more)
Visualizing trajectories with PyMOL
Tuesday, March 20, 2012
Previously, we looked at how to visualize color-coded trajectories in VMD. Today we’ll look at how we can accomplish a similar effect with PyMOL.   First, assuming your trajectory is starting out as an xyz coordinate file, you can convert it to a pdb format with the OpenBabel software package. ... (read more)
Including Hubbard U variations with DFT+U(R)
Tuesday, February 21, 2012
The Hubbard U may be straightforwardly calculated from linear response and will vary depending upon the configuration and coordination environment of the transition metal in question.  However, results at differing values of U are challenging to compare so most typically we average the calculated... (read more)
A review of DFT+U
Tuesday, February 14, 2012
It’s just a couple more weeks until the 2012 march meeting of the American Physical Society in Boston, MA.  Before the meeting, I’ll put up one more tutorial related to the work that I will be presenting at APS. In the meantime, here are some recent slides I put together that provide an overview of... (read more)
Population analysis and PDOS
Tuesday, January 24, 2012
For molecules and the condensed phase alike, it can be useful to analyze how molecular states are defined by the relative atomic contributions. Visualizing molecular orbitals allows us to identify the overall character of each individual orbital.  However, for larger molecules, it may be... (read more)

Pages

About Us

The Kulik group focuses on the development and application of new electronic structure methods and atomistic simulations tools in the broad area of catalysis.

Our Interests

We are interested in transition metal chemistry, with applications from biological systems (i.e. enzymes) to nonbiological applications in surface science and molecular catalysis.

Our Focus

A key focus of our group is to understand mechanistic features of complex catalysts and to facilitate and develop tools for computationally driven design.

Contact Us

Questions or comments? Let us know! Contact Dr. Kulik: