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 ...
Projects in the Pipeline
A few of the projects on my mind right now. Some are father along than others.
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 ...