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)!

Summer migration and hiatus
Tuesday, June 25, 2013
It’s the summer so posts will slow down a little. In the meantime, there are a few older tutorial entries that use scripts that were written for Quantum-ESPRESSO 4.x. As most of you have upgraded to Q-E 5.0 and there are small changes in how the input and output are parsed, some of these scripts... (read more)
Ten research tools and shortcuts
Tuesday, May 21, 2013
While this month’s tutorial is currently stuck in debugging, here is a list of ten useful things I’ve learned or used in the past few months.  Why not share some useful tips you’ve learned with me? I’ll post the best suggestions on this site. In no particular order, here they are:   10.Generating... (read more)
Building slab geometries for catalysis with VESTA
Tuesday, April 23, 2013
In order to study systems relevant to heterogeneous catalysis, extended supercells of slabs of bulk material must be set up and surrounded by vacuum in order to mimic the properties of an exposed surface. Today, I’ll go over how you can use the program VESTA to set up the initial coordinates for... (read more)
Starting Fall 2013: Kulik group at MIT ChemE
Saturday, April 20, 2013
I’m delighted to announce that I will be starting my own research group at MIT starting in the Fall in the chemical engineering department.  I will continue the tutorials here until my transition to MIT, after which there will likely be some changes in the layout and frequency. I have enjoyed... (read more)
Quick tip: Choosing how to parallelize your jobs
Tuesday, March 19, 2013
In today’s quick tip, we’ll go over why and how you may want to parallelize the jobs that you run.  There are a number of reasons why you may want to parallelize the jobs that you are running.     Why to parallelize: Namely, if your job is large enough, it may simply not fit on a single computer or... (read more)
BIOS 203: Useful commandline tools
Tuesday, February 19, 2013
If you have limited experience with the command line interface (e.g. within a linux installation or Mac OS X’s terminal.app), it can be daunting to find your way around. However, once you get used to the commandline, you’ll often see you can do many things much faster than you would normally be... (read more)
BIOS 203: Preparing proteins
Tuesday, January 29, 2013
The protein databank (PDB) has a wealth of structures that have been solved through x-ray crystallography or NMR.  Often when we are simulating proteins, we start directly from such structures in order to infer electronic and geometric properties of these proteins.  Many times, we still need to do... (read more)
Introducing BIOS 203
Tuesday, December 25, 2012
I will be teaching a mini-course in atomistic simulations at Stanford University called BIOS 203 starting in end of February 2013.  In preparation, the next four tutorials will take on a dual role of supporting the course at Stanford. The course will emphasize the use of Amber, an open source MM... (read more)
Job management 101
Tuesday, November 27, 2012
Today, I’ll take a brief detour from simulations with Quantum-ESPRESSO to take a general look at handy tools for keeping track of the jobs that we run and collecting simulations results. This is by no means a complete list of tools, but it should be helpful to those of you getting started in... (read more)
Quick tip: Maximally localized Wannier functions
Tuesday, October 23, 2012
Using hydrocarbons, today we’ll go over the basics of constructing and visualizing Maximally localized Wannier functions as a tool for understanding bonding in molecules.  All of our calculations use the Wannier90 tool, which has its own tutorials and examples provided with the PW code that you may... (read more)

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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: