Background and Motivation
Conformation Dynamics with MSMBuilder
The goals
Workflow
Installation
Installation
Dependencies
Frequently Asked Questions
I get a wierd error during compilation with
pip
install
or
python
setup.py
install
. What’s wrong?
Do I need Anaconda python? Can’t I use the python that comes with my operating like
/usr/bin/python
?
How do I get (quickly) started on Windows?
Changelog
v3.1 (Feb 27, 2015)
v3.0.1 (January 9, 2015)
v3.0.0 (January 9, 2015)
Examples
Bayesian Estimation of MSMs
GMRQ hyperparameter selection
HMM and MSM Timescales for Ala2
Implied Timescales
Visualization with tICA
Bootstraped MSM CIs
Model selection with Randomized CV
tICA and PCA
Estimating uncertainty in Markov state models
Featurization and Distance Metrics
Background
Featurizations
Distance Metrics
Geometric Clustering
Background
API and Implementation Notes
Algorithms
Additional Algorithms
Example
References
Markov state models (MSMs)
Background
Algorithms
Maximum Likelihood and Bayesian Estimation
Tradeoffs and Parameter Selection
Analyzing an MSM
References
Continuous-time Markov State Model
Algorithms
Theory
Dense Parameterization
Sparse Parameterization
Estimation
Under the hood (expert functions)
References
Transition Path Theory
Background
Functions
Time-structure Independent Components Analysis (tICA)
Background
Algorithms
Combination with MSM
Example
References
Hidden Markov models (HMMs)
Background
L1-Regularized Reversible Gaussian HMM
Algorithms
Example
References
Datasets and Persistence
Datasets
Model persistence
Functions
Command Line Tutorial
Tutorial
MSMBuilder API Patterns
MSMBuilder API
Pipelines
Extending MSMBuilder with Plugins
Frequently Asked Questions
How should I get started?
How do I report a bug?
How do I contribute a new feature?
Where should I start with the MSM literature?
What is the relationship between MSMBuilder and other packages?
How much MD sampling do I need to build an MSM?
How can I validate an MSM?
How can statistical models like MSMs be used to accelerate MD?
What are the tradeoffs between running a large number of short MD simulations vs. a few long ones?
My simulations use replica exchange, aMD, or metadynamics. Can I use these tools to analyze them?
Why am I getting MemoryErrors?
How can I cite MSMBuilder?
References
msmbuilder
Docs
»
Overview: module code
Edit on GitHub
All modules for which code is available
msmbuilder.cluster
msmbuilder.dataset
msmbuilder.decomposition
msmbuilder.featurizer
msmbuilder.hmm
msmbuilder.msm
msmbuilder.msm._ratematrix
msmbuilder.tpt
Versions
Development