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  1. MDBenchmark MDBenchmark Public

    Quickly generate, start and analyze benchmarks for molecular dynamics simulations.

    Python 81 17

  2. cnt-gaff cnt-gaff Public

    Build atomistic structures of carbon nanotubes with the possibility to add functional groups (OH, COOH, COO-) and assigns generalized Amber (GAFF) parameters to them.

    Rich Text Format 24 8

  3. pydiffusion pydiffusion Public

    Analyse Rotational Diffusion Tensor from MD Simulations

    Jupyter Notebook 22 4

  4. BioEn BioEn Public

    BioEn - Bayesian Inference Of ENsembles

    Python 22 10

  5. aimmd aimmd Public

    aimmd (AI for Molecular Mechanism Discovery) autonomously steers (a large number of) molecular dynamics simulations to efficiently sample and understand rare transition events.

    Python 21 2

  6. PyDHAMed PyDHAMed Public

    Dynamic Histogram Analysis To Determine Free Energies and Rates from Biased Simulations

    Jupyter Notebook 20 7

Repositories

Showing 10 of 43 repositories
  • asyncmd Public

    asyncmd is a library to write concurrent code to run and analyze molecular dynamics simulations using pythons async/await syntax. Computationally costly operations can be performed locally or submitted to a queuing system.

    bio-phys/asyncmd’s past year of commit activity
    Python 20 GPL-3.0 4 1 1 Updated Dec 15, 2025
  • aimmd Public

    aimmd (AI for Molecular Mechanism Discovery) autonomously steers (a large number of) molecular dynamics simulations to efficiently sample and understand rare transition events.

    bio-phys/aimmd’s past year of commit activity
    Python 21 GPL-3.0 2 0 1 Updated Nov 22, 2025
  • polyUb-AF Public
    bio-phys/polyUb-AF’s past year of commit activity
    Jupyter Notebook 4 0 0 0 Updated Jul 21, 2025
  • bio-phys/nix-lir-binding-to-wipi2d’s past year of commit activity
    Jupyter Notebook 0 MIT 0 0 0 Updated Jun 23, 2025
  • trimem Public

    Monte Carlo sampling of the Helfrich bending energy.

    bio-phys/trimem’s past year of commit activity
    C++ 7 GPL-3.0 4 0 2 Updated May 22, 2025
  • af2_lir_screen Public

    AlphaFold2 Multimer pipeline to identify candidate LIR motifs

    bio-phys/af2_lir_screen’s past year of commit activity
    Python 1 GPL-3.0 0 0 0 Updated Jan 17, 2025
  • pydiffusion Public

    Analyse Rotational Diffusion Tensor from MD Simulations

    bio-phys/pydiffusion’s past year of commit activity
    Jupyter Notebook 22 4 0 0 Updated Oct 31, 2024
  • MDBenchmark Public

    Quickly generate, start and analyze benchmarks for molecular dynamics simulations.

    bio-phys/MDBenchmark’s past year of commit activity
    Python 81 17 11 4 Updated Sep 5, 2024
  • hierarchical-chain-growth Public

    Grow ensembles of disordered biomolecules from fragment libraries

    bio-phys/hierarchical-chain-growth’s past year of commit activity
    Python 9 GPL-3.0 1 1 0 Updated Jul 24, 2024
  • BioEn.jl Public

    BioEn optimization

    bio-phys/BioEn.jl’s past year of commit activity
    Julia 0 MIT 0 0 0 Updated Apr 19, 2024

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