Pinned Repositories
Clustering
Robust and stable clustering of molecular dynamics simulation trajectories.
dcTMD
Analysis framework of dissipation-corrected targeted molecular dynamics (dcTMD) simulations.
dcTMD_scripts_v1.0
dissipation corrected targeted molecular dynamics
FastPCA
Fast, parallelized implementation of Principal Component Analysis with constant memory consumption for large data sets.
HP35
Selecting Features for Markov Modeling: A Case Study on HP35
HP35-DESRES
DESRES trajectory of wild type HP-35 at 360K
MoSAIC
Correlation-based feature selection of Molecular Dynamics simulations
msmhelper
Helper function for Markov State Models
MSMPathfinder
Finding pathways from an Markov State Model
NorMI
Generalized Kraskov Estimator for Normalized Mutual Information
Biomolecular Dynamics's Repositories
moldyn/MoSAIC
Correlation-based feature selection of Molecular Dynamics simulations
moldyn/Clustering
Robust and stable clustering of molecular dynamics simulation trajectories.
moldyn/dcTMD
Analysis framework of dissipation-corrected targeted molecular dynamics (dcTMD) simulations.
moldyn/FastPCA
Fast, parallelized implementation of Principal Component Analysis with constant memory consumption for large data sets.
moldyn/MSMPathfinder
Finding pathways from an Markov State Model
moldyn/NorMI
Generalized Kraskov Estimator for Normalized Mutual Information
moldyn/HP35
Selecting Features for Markov Modeling: A Case Study on HP35
moldyn/msmhelper
Helper function for Markov State Models
moldyn/HP35-DESRES
DESRES trajectory of wild type HP-35 at 360K
moldyn/Data-Driven-Langevin
Program to run the data driven Langevin equation as described in Schaudinnus et al., Phys. Rev. Lett. 115, 050602 (2015) or Rzepiela et al. J. Chem. Phys. 141, 241102 (2014). The basic publication is Hegger and Stock, J. Chem. Phys. 130, 034106 (2009) .
moldyn/dcTMD_scripts_v1.0
dissipation corrected targeted molecular dynamics
moldyn/tutorial_dcTMD
Tutorial for the usage of the dcTMD approach and Langevin simulations employing the trypsin-benzamidine complex as example.
moldyn/2Dmodel_path_analysis
Jupyter notebook with 2D test potential energy landscape for performing model biased simulations combined with pathway analysis.
moldyn/HP35-Benchmark
Benchmarking dimensionality reduction methods and clustering on HP35-DESRES
moldyn/ramacolor
The ramacolor script produce plots as proposed in Sittel et al., J. Chem. Theory Comput 12, 2426 (2016)
moldyn/.github
moldyn/forceatlas2
Fastest Gephi's ForceAtlas2 graph layout algorithm implemented for Python and NetworkX
moldyn/Langevin_T_boost
Includes C++ code to run Markovian Langevin equations in units compatible with the dcTMD correction scripts available at www.moldyn.uni-freiburg.de/software/software.html. In addition, a jupyter notebook can be found which estimates the error of rates at 300 K from T-boosting calculations.
moldyn/python-packaging
An example python packaging
moldyn/rescaled_dLE_and_pre_averaging
Includes implementations of the data-driven Langevin equation with and without rescaling of the friction. Includes also data-driven Langevin codes which work with pre-averaged data. Finally, programs can be found to produce Markovian and generalized Langevin dynamics in case the fields are already known. The generalized Langevin equation assumes a mono-exponential memory kernel.
moldyn/xgbAnalysis
Machine-Learning analysis of large data sets from molecular dynamics simulation