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)!

molSimplify Tutorial 6: Placing structures on slabs
Friday, March 10, 2017
In this follow up to our first tutorial , we are going to describe how to use molSimplify to control the placement of molecules, atoms and complexes on surfaces. We’ll assume you have followed the last tutorial and have a file containing the xyz coordinates of your surface (you might want to relax... (read more)
molSimplify Tutorial 5: Using machine learning to build better structures
Monday, February 27, 2017
We have recently implemented an artificial neural network (ANN) in molSimplify – you can read all about it in our recent Chemical Science paper here, but the basic principle is easy to understand. We first collected information from 2700 transition metal complexes that we optimized using DFT, and... (read more)
molSimplify Tutorial 3: Custom Core Functionalization
Sunday, December 25, 2016
In this tutorial, we'll show how to use molSimplify's custom core functionalization feature. This feature allows new functional groups (FGs) or ligands to be attached to user-specified positions in existing structures, and is most useful for studying the effects of ligand functionalization on... (read more)
molSimplify Tutorial 4: Database Searching
Sunday, December 25, 2016
In this tutorial, we'll show how to use molSimplify to perform chemical database screening, leveraging on calls to OpenBabel together with useful preprocessing and postprocessing tools for seamless integration with the rest of the molSimplify package. Today, we will demonstrate how to search a... (read more)
Guide to Charge Shift Analysis and Fukui Shift Analysis
Tuesday, December 13, 2016
Here, we outline the procedure for our recently developed CSA and FSA methods, which provide systematic methods for determining QM region in QM/MM simulation. 1. In charge shift analysis, we introduce the idea that rigidly removing core active site residues and computing the electronic... (read more)
molSimplify Tutorial 2: Slab Builder
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 1: Structure Generation
Saturday, June 18, 2016
In our first tutorial, we'll briefly discuss how to use molSimplify to generate simple coordination complexes. Our example today is a cobalt porphyrin with an imidazole axial ligand and an empty 6th coordination site. Graphical User Interface Firstly, we'll show how to use the graphical user... (read more)
molSimplify: introduction
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)

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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: