Repositories list

• asyncmd

  Public
  asyncmd is a library to write concurrent code to run and analyze molecular dynamics simulations using pythons async/await syntax. Computationally costly operati…

  molecular-dynamicsslurmmolecular-dynamics-simulation+ 2

  molecular-dynamicsslurmmolecular-dynamics-simulationslurm-clusterenhanced-sampling

  Python

  •

  GNU General Public License v3.0

  •44 forks•2020 stars•11 issue•11 pull request•Updated Apr 9, 2026Apr 9, 2026

• aimmd

  Public
  aimmd (AI for Molecular Mechanism Discovery) autonomously steers (a large number of) molecular dynamics simulations to efficiently sample and understand rare tr…

  Python

  •

  GNU General Public License v3.0

  •22 forks•2121 stars•00 issues•11 pull request•Updated Nov 22, 2025Nov 22, 2025

• polyUb-AF

  Public
  Jupyter Notebook

  •

  Other

  •00 forks•44 stars•00 issues•00 pull requests•Updated Jul 21, 2025Jul 21, 2025

• nix-lir-binding-to-wipi2d

  Public
  md-simulationsanalysis-scripts

  md-simulationsanalysis-scripts

  Jupyter Notebook

  •

  MIT License

  •00 forks•00 stars•00 issues•00 pull requests•Updated Jun 23, 2025Jun 23, 2025

• trimem

  Public
  Monte Carlo sampling of the Helfrich bending energy.

  C++

  •

  GNU General Public License v3.0

  •44 forks•77 stars•00 issues•22 pull requests•Updated May 22, 2025May 22, 2025

• af2_lir_screen

  Public
  AlphaFold2 Multimer pipeline to identify candidate LIR motifs

  alphafold2lc3-liratg8-aim

  alphafold2lc3-liratg8-aim

  Python

  •

  GNU General Public License v3.0

  •00 forks•11 star•00 issues•00 pull requests•Updated Jan 17, 2025Jan 17, 2025

• pydiffusion

  Public
  Analyse Rotational Diffusion Tensor from MD Simulations

  pythonsimulationmolecular-dynamics+ 4

  pythonsimulationmolecular-dynamicsrotationmdanalysisdiffusionbrownian-dynamics

  Jupyter Notebook

  •

  Other

  •44 forks•2222 stars•00 issues•00 pull requests•Updated Oct 31, 2024Oct 31, 2024

• MDBenchmark

  Public

  bio-phys/MDBenchmark’s past year of commit activity
  Quickly generate, start and analyze benchmarks for molecular dynamics simulations.

  pythonclibenchmark+ 6

  pythonclibenchmarksimulationmolecular-dynamicscomputational-chemistryhigh-performance-computingnamdgromacs

  Python

  •

  Other

  •1717 forks•8383 stars•1111 issues•44 pull requests•Updated Sep 5, 2024Sep 5, 2024

• hierarchical-chain-growth

  Public
  Grow ensembles of disordered biomolecules from fragment libraries

  Python

  •

  GNU General Public License v3.0

  •11 fork•99 stars•11 issue•00 pull requests•Updated Jul 24, 2024Jul 24, 2024

• BioEn.jl

  Public
  BioEn optimization

  Julia

  •

  MIT License

  •00 forks•00 stars•00 issues•00 pull requests•Updated Apr 19, 2024Apr 19, 2024

• BioEn

  Public
  BioEn - Bayesian Inference Of ENsembles

  structural-biologymolecular-dynamicsbiological-simulations+ 8

  structural-biologymolecular-dynamicsbiological-simulationsnmrdata-integrationbayesian-inferencedeerxray-scattering-experimentselectron-paramagnetic-resonancesaxs+ 1

  Python

  •

  Other

  •1010 forks•2424 stars•11 issue•55 pull requests•Updated Feb 6, 2024Feb 6, 2024

• RefinementModels.jl

  Public
  Julia

  •

  MIT License

  •00 forks•00 stars•00 issues•00 pull requests•Updated Oct 12, 2023Oct 12, 2023

• VantHoffFitting

  Public
  Nonlinear least squares fitting of van 't Hoff plots via cubic splines, which makes the extraction of heat capacity and thermodynamic potentials possible.

  Julia

  •

  MIT License

  •11 fork•00 stars•00 issues•55 pull requests•Updated Aug 7, 2023Aug 7, 2023

• ForceSpectroscopyMLE

  Public
  Analyze rupture force spectra from single-molecule force spectroscopy experiments to extract disassociation rates and parameters characterizing the free-energy …

  juliamaximum-likelihood-estimationsingle-molecule-force-spectroscopy+ 1

  juliamaximum-likelihood-estimationsingle-molecule-force-spectroscopyforcible-bond-rupture

  Julia

  •

  GNU General Public License v3.0

  •11 fork•22 stars•00 issues•55 pull requests•Updated Aug 7, 2023Aug 7, 2023

• complexespp

  Public
  Coarse-grained simulations of biomolecular complexes

  C++

  •

  Other

  •55 forks•1313 stars•1010 issues•11 pull request•Updated Aug 2, 2023Aug 2, 2023

• SAXS_BioEn

  Public
  Jupyter Notebook

  •

  MIT License

  •00 forks•22 stars•00 issues•00 pull requests•Updated Jul 11, 2023Jul 11, 2023

• ForceFieldsMC3

  Public
  00 forks•11 star•00 issues•00 pull requests•Updated Jun 23, 2023Jun 23, 2023

• BioEM

  Public
  GPU accelerating computing for Bayesian inference of electron microscopy images. BioEM is a publicly available software that enables the characterization of str…

  C++

  •

  Other

  •33 forks•1111 stars•22 issues•11 pull request•Updated Apr 7, 2023Apr 7, 2023

• constraint-coupling-analysis

  Public
  Python

  •00 forks•33 stars•00 issues•00 pull requests•Updated Oct 17, 2022Oct 17, 2022

• cnt-clusters

  Public
  Simulation parameters and results for lipid-mediated self-assembly of CNT membranes.

  OpenEdge ABL

  •11 fork•00 stars•00 issues•00 pull requests•Updated Aug 21, 2022Aug 21, 2022

• DiffusionGLS

  Public
  Estimate the self-diffusion coefficient of a trajectory with a Generalized Least Squares (GLS) optimization procedure.

  Jupyter Notebook

  •

  GNU General Public License v3.0

  •88 forks•1616 stars•22 issues•22 pull requests•Updated Aug 12, 2022Aug 12, 2022

• memdiff

  Public
  Implementation of corrections for diffusion coefficients in membrane simulations.

  diffusion-coefficientmembrane-simulationslipid-membranes

  diffusion-coefficientmembrane-simulationslipid-membranes

  Python

  •

  MIT License

  •11 fork•1010 stars•00 issues•00 pull requests•Updated Aug 2, 2022Aug 2, 2022

• RebindingKineticsMLE

  Public
  Analyze pulling traces from single-molecule force spectroscopy experiments close to equilibrium to extract on and off rates and parameters characterizing the fr…

  Julia

  •

  GNU General Public License v3.0

  •11 fork•11 star•00 issues•11 pull request•Updated Jul 18, 2022Jul 18, 2022

• ff-Mg-Ca-NucleicAcids

  Public
  Extension for the interactions with DNA and RNA of our previously bulk-optimized force field parameters (https://doi.org/10.1063/1.5017694)

  11 fork•00 stars•11 issue•00 pull requests•Updated Jun 23, 2022Jun 23, 2022

• BioFF

  Public
  Bayesian inference of force fields

  Jupyter Notebook

  •00 forks•11 star•00 issues•00 pull requests•Updated Dec 22, 2021Dec 22, 2021

• MgFF_OPC

  Public
  Magnesium Force Fields for OPC Water with Accurate Solvation, Ion-Binding, and Water-Exchange Properties: Successful Transfer from SPC/E

  00 forks•11 star•11 issue•00 pull requests•Updated Dec 9, 2021Dec 9, 2021

• optimizedMgFFs

  Public
  Optimized force field parameters for Magnesium in combination with the SPC/E, TIP3P-fb, TIP4P/2005, TIP4P-Ew, or TIP4P-D water model for all-atom MD simulations…

  00 forks•44 stars•22 issues•00 pull requests•Updated Dec 9, 2021Dec 9, 2021

• Magnesium-FFs

  Public
  Optimized force field parameters for Magnesium in combination with the TIP3P water model for all-atom MD simulations.

  Makefile

  •00 forks•55 stars•11 issue•00 pull requests•Updated Dec 2, 2021Dec 2, 2021

• cnt-martini

  Public
  Generates Martini models for open carbon nanotubes to use with Gromacs.

  Python

  •

  MIT License

  •44 forks•1515 stars•11 issue•00 pull requests•Updated Nov 24, 2021Nov 24, 2021

• DiffusionMLE

  Public
  Analyze experimental tracking data using a maximum likelihood estimator (MLE) to extract translational diffusion coefficients.

  juliaexpectation-maximization-algorithmdiffusion-coefficient+ 1

  juliaexpectation-maximization-algorithmdiffusion-coefficientmaximum-likelihood-estimation

  Julia

  •

  GNU General Public License v3.0

  •22 forks•22 stars•00 issues•55 pull requests•Updated Sep 28, 2021Sep 28, 2021