HP35-Benchmark

Benchmarking dimensionality reduction methods and clustering on HP35-DESRES.

This is package automatizes the comparison of different clustring and dimensionality reduction methods and its effects on the resulting Markov state models. So far, only the result of Nagel et al. 19 are reproduced. Comparison methods will follow soon.

If the provided scripts are used, please cite:

• D. Nagel, A. Weber, B. Lickert and G. Stock, Dynamical coring of Markov state models, J. Chem. Phys., 150, 094111, 2019; DOI: 10.1063/1.5081767

Getting ready

Simply clone this repository with

git clone --recurse-submodules git://github.com/moldyn/HP35-Benchmark.git
cd HP35-Benchmark

Reproducing the published state trajectory can be achieved with

cd clustering && bash robust_clustering

Until our python package msmhelper is available, the states are not renamed by their population.

Add Own Routine

For an example take a look at robust_clustering