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    37 repositories

    • kimmdy-examples

      Public
      KIMMDY examples, analysis, figures etc. to go along with the manuscript
      Python
      •0•0•0•0•Updated Feb 25, 2026Feb 25, 2026

    • kimmdy-examples-release

      Public
      KIMMDY examples, analysis, figures etc. to go along with the manuscript
      Python
      •0•0•0•0•Updated Feb 25, 2026Feb 25, 2026

    • kimmdy-dimerization-examples

      Public
      Examples displaying the usage of the kimmdy-dimerization plugin
      Python
      •0•0•0•0•Updated Feb 25, 2026Feb 25, 2026

    • kimmdy-n-alkyl-radicals_examples

      Public
      Python
      •0•0•0•0•Updated Feb 25, 2026Feb 25, 2026

    • kimmdy-hat

      Public
      KIMMDY plugin for Hydrogen Atom Transfer
      kimmdy
      PureBasic
      •
      GNU General Public License v3.0
      •2•2•3•0•Updated Feb 24, 2026Feb 24, 2026

    • kimmdy-hydrolysis-examples

      Public
      A collection of KIMMDY examples to demonstrate the interplay between various kimmdy plugins
      Python
      •0•3•0•0•Updated Feb 24, 2026Feb 24, 2026

    • colbuilder

      Public
      Building collagen fibrils from amino acids sequences
      modelingcollagen
      Python
      •
      Apache License 2.0
      •2•6•2•3•Updated Feb 13, 2026Feb 13, 2026

    • DNAHairpins

      Public
      Supplementary Code for Mechanochemistry of DNA Hairpins
      Python
      •
      GNU General Public License v3.0
      •0•0•0•0•Updated Feb 3, 2026Feb 3, 2026

    • hydrolysis-qmmm-workflow

      Public
      Workflow for QM/MM simulations of collagen triplehelix and single peptide hydrolysis
      JavaScript
      •0•0•0•0•Updated Jan 28, 2026Jan 28, 2026

    • sith

      Public
      Splitting Intramolecular Tension via stretcHing, a novel method that decomposes the total electronic energy change of a stretched molecule into contributions fr…
      Python
      •
      GNU General Public License v3.0
      •1•2•0•0•Updated Jan 21, 2026Jan 21, 2026

    • grappa

      Public
      A machine learned Molecular Mechanics force field with integration into GROMACS and OpenMM
      Python
      •
      GNU General Public License v3.0
      •6•60•5•0•Updated Jan 21, 2026Jan 21, 2026

    • bbflow

      Public
      A flow matching model for generating conformational ensembles of protein backbones.
      Python
      •
      Other
      •1•36•1•0•Updated Jan 7, 2026Jan 7, 2026

    • backflip

      Public
      Fast protein backbone flexibility prediction model
      Python
      •
      Other
      •6•34•0•0•Updated Jan 4, 2026Jan 4, 2026

    • kimmdy

      Public
      Reactive MD pipeline for GROMACS using Kinetic Monte Carlo / Molecular Dynamics (KIMMDY)
      molecular-dynamicskinetic-monte-carlogromacskimmdy
      Python
      •
      GNU General Public License v3.0
      •8•14•43•3•Updated Jan 2, 2026Jan 2, 2026

    • kimmdy-dimerization

      Public
      KIMMDY Plugin for Thymine-Thymine Dimerization in DNA
      kimmdy
      Python
      •
      GNU General Public License v3.0
      •2•2•0•0•Updated Jan 2, 2026Jan 2, 2026

    • gmxtop

      Public
      Python
      •
      Other
      •0•1•0•0•Updated Dec 19, 2025Dec 19, 2025

    • kimmdy-hydrolysis

      Public
      Example custom reaction for KIMMDY that hydrolyses peptide bonds
      kimmdy
      Python
      •
      GNU General Public License v3.0
      •2•1•0•0•Updated Dec 11, 2025Dec 11, 2025

    • kimmdy-grappa

      Public
      KIMMDY plugin for the GRAPPA parameterizer
      kimmdy
      Lua
      •
      GNU General Public License v3.0
      •1•2•2•2•Updated Sep 9, 2025Sep 9, 2025

    • IM30_alpha1-3

      Public
      Python
      •
      GNU General Public License v3.0
      •0•0•0•0•Updated Sep 8, 2025Sep 8, 2025

    • kimmdy-reactions

      Public
      Builtin reactions for KIMMDY
      kimmdy
      Python
      •
      GNU General Public License v3.0
      •2•2•2•0•Updated Aug 11, 2025Aug 11, 2025

    • flips

      Public
      Flexibility-conditioned protein structure design
      Python
      •
      Other
      •0•32•1•0•Updated Jul 5, 2025Jul 5, 2025

    • kimmdy_paper_theme

      Public
      Theme elements for the KIMMDY paper
      Python
      •0•2•0•0•Updated Jul 3, 2025Jul 3, 2025

    • grappa-tabulated-forcefields

      Public
      Classical force fields from Grappa models for GROMACS oder OpenMM
      Python
      •
      GNU General Public License v3.0
      •0•0•0•0•Updated Feb 7, 2025Feb 7, 2025

    • gromacs-plumed-docker

      Public
      Shell
      •9•0•0•0•Updated Sep 12, 2024Sep 12, 2024

    • g-tensors-PPEpaper

      Public
      Repository containing all the codes and computation of g-values to compare with EPR experiments.
      Jupyter Notebook
      •0•0•0•0•Updated Jun 21, 2024Jun 21, 2024

    • 2024-hits-kimmdy

      Public
      JavaScript
      •0•0•0•0•Updated Jun 3, 2024Jun 3, 2024

    • doc_template

      Public
      Documentation template using MkDocs
      1•0•0•0•Updated May 29, 2024May 29, 2024

    • kimmdy-HAT-fixed-rate

      Public
      KIMMDY HAT reaction plugin with fixed rate
      Python
      •
      GNU General Public License v3.0
      •0•1•0•0•Updated Mar 21, 2024Mar 21, 2024

    • AAmatcher

      Public
      Package to convert structures from g09 logfiles to gromacs convertible pdb files
      Python
      •
      MIT License
      •0•2•0•0•Updated Jul 3, 2023Jul 3, 2023

    • paper-talin-loop

      Public
      HTML
      •1•4•0•0•Updated Jun 17, 2023Jun 17, 2023