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@moldyn Biomolecular Dynamics

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    23 repositories

    • NorMI

      Public
      Generalized Kraskov Estimator for Normalized Mutual Information
      Python
      •
      MIT License
      •2•21•3•0•Updated Dec 16, 2025Dec 16, 2025

    • dcTMD

      Public
      Analysis framework of dissipation-corrected targeted molecular dynamics (dcTMD) simulations.
      pythonbiomolecular-dynamicsbiasing-md-simulations
      Python
      •
      MIT License
      •1•15•0•0•Updated Dec 16, 2025Dec 16, 2025

    • MoSAIC

      Public
      Correlation-based feature selection of Molecular Dynamics simulations
      Python
      •
      MIT License
      •3•29•0•0•Updated Nov 25, 2025Nov 25, 2025

    • MPP

      Public
      Implementation of the Most Probable Path (MPP) algorithm for the coarse-graining of state trajectories, e.g. as obtained from Molecular Dynamics simulations.
      Python
      •
      MIT License
      •0•0•0•0•Updated Oct 17, 2025Oct 17, 2025

    • GP-TEMPEST

      Public
      Gaussian Process Temporal Embedding for Protein Simulations and Transitions
      Python
      •0•2•0•0•Updated Oct 13, 2025Oct 13, 2025

    • tutorial_dcTMD

      Public
      Tutorial for the usage of the dcTMD approach and Langevin simulations employing the trypsin-benzamidine complex as example.
      Python
      •
      GNU General Public License v3.0
      •4•2•0•0•Updated Jul 15, 2024Jul 15, 2024

    • msmhelper

      Public
      Helper function for Markov State Models
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •3•12•0•1•Updated Jun 25, 2024Jun 25, 2024

    • HP35

      Public
      Selecting Features for Markov Modeling: A Case Study on HP35
      markov-modelprotein-foldingbenchmark-systemhp35
      HiveQL
      •
      BSD 3-Clause "New" or "Revised" License
      •2•11•2•0•Updated May 25, 2023May 25, 2023

    • HP35-DESRES

      Public
      DESRES trajectory of wild type HP-35 at 360K
      Other
      •0•5•0•0•Updated May 16, 2023May 16, 2023

    • 2Dmodel_path_analysis

      Public
      Jupyter notebook with 2D test potential energy landscape for performing model biased simulations combined with pathway analysis.
      Jupyter Notebook
      •1•1•0•0•Updated Jan 16, 2023Jan 16, 2023

    • Clustering

      Public
      Robust and stable clustering of molecular dynamics simulation trajectories.
      cppclusteringcudamolecular-dynamicsbiophysics
      C++
      •
      BSD 2-Clause "Simplified" License
      •6•19•1•0•Updated Sep 2, 2022Sep 2, 2022

    • HP35-Benchmark

      Public
      Benchmarking dimensionality reduction methods and clustering on HP35-DESRES
      Shell
      •
      BSD 3-Clause "New" or "Revised" License
      •0•1•0•0•Updated Aug 5, 2022Aug 5, 2022

    • MSMPathfinder

      Public
      Finding pathways from an Markov State Model
      cpppathfindingmsmmarkov-chain-monte-carlopath-sampling
      C++
      •
      MIT License
      •3•10•0•0•Updated Jul 29, 2022Jul 29, 2022

    • .github

      Public
      1•0•0•0•Updated Jul 28, 2022Jul 28, 2022

    • dcTMD_scripts_v1.0

      Public
      dissipation corrected targeted molecular dynamics
      Python
      •
      GNU General Public License v3.0
      •6•2•0•0•Updated Mar 10, 2022Mar 10, 2022

    • FastPCA

      Public
      Fast, parallelized implementation of Principal Component Analysis with constant memory consumption for large data sets.
      C
      •
      Other
      •4•11•0•0•Updated Feb 18, 2022Feb 18, 2022

    • python-packaging

      Public
      An example python packaging
      Python
      •
      MIT License
      •0•0•0•0•Updated Dec 2, 2021Dec 2, 2021

    • Langevin_T_boost

      Public
      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.
      Jupyter Notebook
      •
      GNU General Public License v3.0
      •4•0•0•0•Updated Sep 24, 2021Sep 24, 2021

    • xgbAnalysis

      Public
      Machine-Learning analysis of large data sets from molecular dynamics simulation
      R
      •
      BSD 2-Clause "Simplified" License
      •2•0•1•0•Updated May 21, 2021May 21, 2021

    • forceatlas2

      Public
      Fastest Gephi's ForceAtlas2 graph layout algorithm implemented for Python and NetworkX
      Python
      •
      GNU General Public License v3.0
      •87•0•0•0•Updated Nov 4, 2020Nov 4, 2020

    • rescaled_dLE_and_pre_averaging

      Public
      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…
      C++
      •
      GNU General Public License v3.0
      •1•0•0•0•Updated Oct 8, 2020Oct 8, 2020

    • ramacolor

      Public
      The ramacolor script produce plots as proposed in Sittel et al., J. Chem. Theory Comput 12, 2426 (2016)
      Python
      •
      BSD 2-Clause "Simplified" License
      •2•1•0•0•Updated Feb 13, 2020Feb 13, 2020

    • Data-Driven-Langevin

      Public
      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) .
      C
      •
      GNU General Public License v3.0
      •1•3•0•0•Updated Jan 8, 2019Jan 8, 2019