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 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) 

Quick tips: More about U Saturday, November 30, 2013 This month marked both the AIChE national meeting in San Francisco's special symposium that I coorganized called "Applications of DFT+X in catalysis" as well as my first month as an assistant professor. The tutorials are likely to be archived and remain online but will no longer be updated as... (read more) 

Geometries from strings with SMILES and OpenBabel Tuesday, October 29, 2013 When we carry out simulations, one of the first things we need to do is to build the molecules that we want to study. This step can be arduous for complex systems where existing experimental structures are not available (i.e. proteins from the protein databank, molecular structures from the... (read more) 