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@moldyn Biomolecular Dynamics

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    25 repositories

    • dcTMD

      Public
      Analysis framework of dissipation-corrected targeted molecular dynamics (dcTMD) simulations.
      pythonbiomolecular-dynamicsbiasing-md-simulations
      pythonbiomolecular-dynamicsbiasing-md-simulations
      Python
      •
      MIT License
      •2•17•0•0•Updated Oct 27, 2026Oct 27, 2026

    • NorMI

      Public
      Generalized Kraskov Estimator for Normalized Mutual Information
      Python
      •
      MIT License
      •2•23•1•3•Updated Oct 24, 2026Oct 24, 2026

    • contacts-routine

      Public
      Routine to compute contact distances from MD trajectory
      Python
      •1•0•0•0•Updated Oct 7, 2026Oct 7, 2026

    • TimeScaleAnalysis

      Public
      Python
      •0•0•0•0•Updated Sep 15, 2026Sep 15, 2026

    • MoSAIC

      Public
      Correlation-based feature selection of Molecular Dynamics simulations
      Python
      •
      MIT License
      •3•29•0•0•Updated Aug 18, 2026Aug 18, 2026

    • 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•2•0•0•Updated Jun 23, 2026Jun 23, 2026

    • GP-TEMPEST

      Public
      Gaussian Process Temporal Embedding for Protein Simulations and Transitions
      Python
      •
      Other
      •0•2•0•0•Updated May 4, 2026May 4, 2026

    • 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•11•0•1•Updated Jun 25, 2024Jun 25, 2024

    • HP35

      Public
      Selecting Features for Markov Modeling: A Case Study on HP35
      markov-modelprotein-foldingbenchmark-system
      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•8•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.
      cppclusteringcuda
      cppclusteringcudamolecular-dynamicsbiophysics
      C++
      •
      BSD 2-Clause "Simplified" License
      •6•20•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
      cpppathfindingmsm
      cpppathfindingmsmmarkov-chain-monte-carlopath-sampling
      C++
      •
      MIT License
      •3•9•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•12•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/sof…
      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
      •89•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 wi…
      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,…
      C
      •
      GNU General Public License v3.0
      •1•3•0•0•Updated Jan 8, 2019Jan 8, 2019
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