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  1. MDBenchmark MDBenchmark Public

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

    Python 80 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 23 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 21 10

  5. PyDHAMed PyDHAMed Public

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

    Jupyter Notebook 20 7

  6. asyncmd 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 submi…

    Python 19 4

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 19 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 19 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 80 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