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    20 repositories

    • colbuilder

      Public
      Building collagen fibrils from amino acids sequences
      modelingcollagen
      Python
      •
      Apache License 2.0
      •0•0•0•0•Updated Oct 31, 2024Oct 31, 2024

    • grappa

      Public
      A Machine Learned Molecular Mechanics Force Field with integration into GROMACS and OpenMM
      Python
      •
      GNU General Public License v3.0
      •0•33•1•0•Updated Oct 24, 2024Oct 24, 2024

    • 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
      •1•8•41•4•Updated Oct 23, 2024Oct 23, 2024

    • kimmdy-reactions

      Public
      Builtin reactions for KIMMDY
      kimmdy
      Python
      •
      GNU General Public License v3.0
      •1•2•2•1•Updated Sep 30, 2024Sep 30, 2024

    • gromacs-plumed-docker

      Public
      Shell
      •6•0•0•0•Updated Sep 12, 2024Sep 12, 2024

    • kimmdy-grappa

      Public
      KIMMDY plugin for the GRAPPA parameterizer
      kimmdy
      Lua
      •
      GNU General Public License v3.0
      •0•2•1•0•Updated Sep 6, 2024Sep 6, 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

    • SITH

      Public
      Stress Induced Traversal of Hessian analysis, a refactorization of JEDI to analyze distribution of energy in molecules under a stress force.
      HTML
      •
      GNU General Public License v3.0
      •0•2•0•0•Updated Feb 21, 2024Feb 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

    • nglview_demo

      Public
      notebok introducing nglview
      Jupyter Notebook
      •0•1•0•0•Updated Apr 20, 2023Apr 20, 2023

    • hits-quarto

      Public
      HTML
      •
      MIT License
      •0•0•0•0•Updated Jan 9, 2023Jan 9, 2023

    • kimmdy-poster

      Public
      HTML
      •0•1•0•0•Updated Jul 12, 2022Jul 12, 2022

    • collagen-visualization

      Public
      HTML
      •0•1•0•0•Updated Jun 22, 2022Jun 22, 2022

    • how-to-terminal

      Public
      "Wait, You can do that in a terminal?!" -- tips and tricks for working with the linux terminal and feel like a hacker
      JavaScript
      •
      MIT License
      •0•1•0•0•Updated Jun 14, 2022Jun 14, 2022

    • MA_coll_radicals

      Public
      Code from Wojteks internship on developing ML models for hydrogen atom transfer reaction barrier prediction in collagen.
      Jupyter Notebook
      •
      MIT License
      •1•0•0•0•Updated Apr 23, 2022Apr 23, 2022

    • git-intro

      Public
      Introduction to git and GitHub
      CSS
      •1•1•0•0•Updated Jul 20, 2021Jul 20, 2021