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)!

Slab builder tutorial
Friday, December 2, 2016
  In this tutorial, we are going to introduce the latest molSimplify feature – a tool that allows the construction of periodic geometries and facilitates adsorbing any type of molecule supported by the basic molSimplify onto a slab in various ways. This tool is under development and is only... (read more)
New Installation Option for molSimplify
Monday, October 31, 2016
We are pleased to announce that molSimplify is now available as a Conda package! Conda is a package and environment manager application that lets users easily download and install python, R, C, Scala, Java and other programs, without needing to worry about dependencies. This means getting... (read more)
molSimplify tutorial
Saturday, June 18, 2016
In this tutorial, we'll briefly discuss how to generate and modify complexes within molSimplify and then search for similar ones. We start by pulling up our GUI and entering the options for generating a simple cobalt porphyrin with one imidazole axial ligand and an empty 6th coordination site. The... (read more)
molSimplify
Friday, April 29, 2016
molSimplify is an open source Python code that combines the functionality of Openbabel with new geometric manipulation routines necessary for the generation of transition metal complexes that are then used as input in electronic structure calculations. The software can generate a variety of... (read more)
Fixed atom and boundary condition ab initio molecular dynamics (MD) with TeraChem
Monday, February 8, 2016
In this tutorial, we’ll briefly review how to set up fixed atom or boundary condition molecular dynamics calculations in TeraChem. In a fixed atom molecular dynamics calculation, specified atoms are fixed at their initial positions, without physical movements. These calculations are useful for... (read more)
10.637: Quantum Chemical Simulation, Lecture 3
Monday, August 10, 2015
This is the next lecture in 10.637: Quantum Chemical Simulation, which I taught in Fall 2014 at MIT. This lecture is about geometry optimizations and potential energy surfaces. I will offer this course again in Fall 2015. The course is a mixed theoretical and practical course with six lab exercises... (read more)
Ab initio steered molecular dynamics with TeraChem
Monday, June 8, 2015
Today I'll briefly review how to set up a steered molecular dynamics calculation in TeraChem. In these steered molecular dynamics calculations, specific atoms (attachment points, APs) are pulled at constant force towards pulling points (PPs) that are some distance in space. These calculations are... (read more)
10.637: Quantum Chemical Simulation, Lecture 2
Wednesday, April 22, 2015
This is the first main lecture in 10.637: Quantum Chemical Simulation, which I taught in Fall 2014 at MIT. This lecture is about an introduction to force fields and molecular mechanics. I will offer this course again in Fall 2015. The course is a mixed theoretical and practical course with six lab... (read more)
10.637: Quantum Chemical Simulation, Lecture 1
Tuesday, April 7, 2015
This is an introduction and overview to the course 10.637: Quantum Chemical Simulation, which I taught in Fall 2014 at MIT. I will offer this course again in Fall 2015. The course is a mixed theoretical and practical course with six lab exercises spanning force fields to ab initio molecular... (read more)
Challenges and advances for DFT on GPUs webinar
Friday, April 25, 2014
Here's a link to a recent webinar I gave on some recent work we've done in applying large scale DFT calculations on GPUs with TeraChem. Check out the PDF slides and MP4 of the webinar with audio here. Abstract:Recent advances in reformulating electronic structure algorithms for stream processors... (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: