Robert's Notebook

Computational Chemistry, Python, Politics, Policy

Next Steps With Swift

Let's try doing something a little more complicated with swift. Here's my new swift script. Basically, it's going to run a python script on each of a set of input files

# count.swift
type File;
type Pythonscript;

app (File o) python(Pythonscript script, File input) {
  # this script ...

Setting up Swift

Swift is a parallel scripting language developed at the U. Chicago Computation Institute. It provides a way to manage heterogeneous clusters. I have n jobs that I want to get done, and I have access to about 5 high performance computing clusters. I really dont want to handle file transfer ...

What is the uncertainty in an MSM?

Two major sources of error characterize a Markov state model. The first is the convergence of the dataset -- we can only model the processes that we've simulated, in some form or another. When the sampling is insufficient, its not like the MSM can make something out of nothing. This ...

Faster PyYAML Parsing with LibYAML

This morning, Christian submitted a great pull request to speed up YAML parsing in MSMBuilder using LibYAML. In MSMBuilder, we use a YAML file to save the "project", which is keeps the path to all of the files associated with an MSMBuilder project, such as the different trajectories, and a ...

OpenMM Script Builder

Build custom OpenMM scripts right in the browser! OpenMM is one of the most flexible molecular dynamics packages, put it can be a little intimidating for the new user. Instead of interacting with it via a set of command line scripts, as one would with amber or gromacs, to interact ...

First First-Author Paper

My first first-author paper has just been accepted by the Journal of Chemical Theory and Computation. The title is Learning Kinetic Distance Metrics for Markov State Models of Protein Conformational Dynamics.

Group Meeting

A few weeks ago, I gave the Pande Group meeting. The slides are on github, and you can view them here. The title of the talk is Protein Folding is Easy: Towards Markov State Models for Conformational Change, and mostly addresses my learning distance metrics for kinetic clustering of protein ...

Under One Roof

One of the goals of the MSMBuilder3 development is to make the package as easy to use as possible. Analyzing molecular dynamics is hard enough, so there's no reason that the software should get in your way.

Currently, all of the the MSMBuilder commands are separate scripts that are ...