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)!
Vibrational properties of molecules Tuesday, December 27, 2011 This tutorial will focus on how we can determine the vibrational properties of molecules with PWscf and QuantumESPRESSO using the phonon code. Before we proceed, you’ll need to make sure you have the ph.x executable compiled in your QuantumESPRESSO distribution. If you don’t, type ‘make ph’ at... (read more) 

More visualization with VMD & PyMOL Tuesday, December 13, 2011 As a continuation of the previous tutorial, I will show you a few more things you can do with VMD along with some tricks for PyMOL. We’ll use a model for the phosphopantetheine tether of acyl carrier proteins. This prosthetic tether forms a thioester linkage to amino acids and delivers them to... (read more) 

Visualizing with VMD & rendering with POVRay Tuesday, November 29, 2011 While XCrysden is a great tool for checking your PWscf input for bugs, visualizing NEB pathways and charge densities, this tutorial will show you how VMD can provide powerful tools for visualizing results as well. Getting started with VMD to visualize QuantumESPRESSO results: 1.Choose what you... (read more) 

Calculating Hubbard U for periodic systems Tuesday, November 15, 2011 Periodic systems have always been the primary application for DFT+U. The original utility of DFT+U was largely observed in improving descriptions of band gaps and recovering insulating behavior in materials that standard approximations to DFT make metallic. Previously, I showed you how to calculate... (read more) 

Converging and comparing multiple electronic states Tuesday, November 1, 2011 Multiple lowlying electronic states are common for openshell transition metal complexes and other small molecules. It is important to make sure you can straightforwardly characterize each state you converge to in order to be certain you are obtaining the properties you wish to calculate. In cases... (read more) 

The right Hubbard U for any element Tuesday, October 18, 2011 Thus far, I’ve told you about how to calculate the Hubbard U for single sitesor multiple sites and how to troubleshoot common problems with DFT+U. In fact, calculating U is nearly as easy as carrying out a single point calculation. It is also a powerful tool that gives you information about the... (read more) 

Any requests? Tuesday, September 27, 2011 The next tutorial, which will be an extension to the earlier tutorial on lowlying electronic states, will be ready in the next 12 weeks. In the meantime, I’d like to get some feedback for what you’d like to see more of here. So far, there have been a few tutorials about DFT+U (1,2,3), some... (read more) 

Troubleshooting common problems with DFT+U Tuesday, September 13, 2011 Thus far, I have introduced how to calculate U from linearresponse for both singlesite and multiplesite systems. However, there are a few practical issues you may run into when using DFT+U to study your system. Here is an overview of the most common difficulties and some solutions. 1.“... (read more) 

Intermission Tuesday, August 23, 2011 I will be at the ACS National Meeting in Denver, CO this week presenting work on evaluating protein structure with GPUaccelerated quantum chemistry, the relationship between substrate placement and reactivity in nonheme iron halogenase SyrB2, and an overview of my work in designing catalysts from... (read more) 

Lowlying electronic states Tuesday, August 9, 2011 Open shell species of any kind may have a number of different lowlying electronic states that are all selfconsistent solutions. Even though DFT is a ground state method, it may be applied directly to the lowest electronic state with welldefined quantum numbers, i.e. the lowest energy or ‘ground... (read more) 