Repositories list

• physical_validation

  Public
  Physical validation of molecular simulations

  pythonmolecular-dynamicsmolecular-simulation+ 2

  pythonmolecular-dynamicsmolecular-simulationmolecular-mechanicsphysical-validation

  Python

  •

  MIT License

  •2121 forks•6363 stars•1212 issues•55 pull requests•Updated Apr 6, 2026Apr 6, 2026

• terphenyl_simulations

  Public
  Repository for storing simulation input files and analysis code for terphenyl simulations

  Jupyter Notebook

  •

  MIT License

  •11 fork•00 stars•00 issues•55 pull requests•Updated Mar 16, 2026Mar 16, 2026

• InterMol

  Public
  Conversion tool for molecular simulations

  Python

  •

  MIT License

  •6060 forks•225225 stars•8787 issues•77 pull requests•Updated Jan 22, 2026Jan 22, 2026

• pymbar_notebook_examples

  Public
  Notebooks of pymbar examples

  Jupyter Notebook

  •

  MIT License

  •22 forks•22 stars•00 issues•00 pull requests•Updated Nov 14, 2025Nov 14, 2025

• polymerist

  Public
  Polymer-Oriented LibrarY of Monomer-Expression Rules and In-silico Synthesis Tools

  Python

  •

  MIT License

  •44 forks•11 star•00 issues•00 pull requests•Updated Sep 25, 2025Sep 25, 2025

• Shift_switch_free_energy

  Public
  Shell

  •

  MIT License

  •11 fork•00 stars•00 issues•00 pull requests•Updated Jul 22, 2025Jul 22, 2025

• potatohead

  Public
  links for enhanced sampling papers and code

  11 fork•33 stars•00 issues•00 pull requests•Updated Jul 14, 2025Jul 14, 2025

• FAS

  Public
  Studying Fatty Acid Biosynthesis using Computational Methods

  MATLAB

  •

  MIT License

  •22 forks•00 stars•00 issues•00 pull requests•Updated Jul 9, 2025Jul 9, 2025

• ensemble_md

  Public
  A python package for performing GROMACS simulation ensembles

  Python

  •

  MIT License

  •44 forks•00 stars•00 issues•00 pull requests•Updated Jul 6, 2025Jul 6, 2025

• Lipids_Best_Practices

  Public
  A description of best practices for fitting lipid force fields to experiments

  TeX

  •00 forks•00 stars•00 issues•00 pull requests•Updated Jun 7, 2025Jun 7, 2025

• solvation_shells

  Public
  Molecular simulations for studying aqueous solvation shells and calculating free energy surfaces along the coordination number

  Jupyter Notebook

  •11 fork•11 star•00 issues•00 pull requests•Updated May 27, 2025May 27, 2025

• scalems_optimizedg

  Public
  Files for test of optimizing dg

  Jupyter Notebook

  •

  MIT License

  •00 forks•00 stars•00 issues•00 pull requests•Updated Nov 12, 2024Nov 12, 2024

• MT-REXEE

  Public
  A shared space to access information related to Multiple Topology Replica Exchange of Expanded Ensemble

  Python

  •11 fork•22 stars•00 issues•00 pull requests•Updated Sep 25, 2024Sep 25, 2024

• openff_examples

  Public
  Example notebooks for carrying out various OpenFF tasks

  Jupyter Notebook

  •

  MIT License

  •00 forks•11 star•00 issues•00 pull requests•Updated Sep 4, 2024Sep 4, 2024

• alchemistry.org

  Public
  Source for alchemistry.org web page

  Jupyter Notebook

  •

  Other

  •00 forks•00 stars•00 issues•00 pull requests•Updated Sep 3, 2024Sep 3, 2024

• OpenFF_Bilayer

  Public
  Jupyter Notebook

  •33 forks•00 stars•00 issues•00 pull requests•Updated Aug 29, 2024Aug 29, 2024

• eyring_model

  Public
  Jupyter Notebook

  •11 fork•00 stars•00 issues•00 pull requests•Updated Aug 26, 2024Aug 26, 2024

• PYR1_Design

  Public
  Accompanying MD simulation files for out papre "Rationalizing diverse binding mechanisms to the same protein fold: insights for ligand recognition and biosensor…

  Python

  •

  MIT License

  •00 forks•00 stars•00 issues•00 pull requests•Updated Mar 22, 2024Mar 22, 2024

• simulation_essentials

  Public
  GitHub repository for lessons on simulations

  Jupyter Notebook

  •

  MIT License

  •00 forks•00 stars•00 issues•00 pull requests•Updated Mar 6, 2024Mar 6, 2024

• NMRLipidsDatabankCode

  Public
  NMRlipids databank with altered code for local analysis

  Jupyter Notebook

  •

  GNU General Public License v3.0

  •3636 forks•00 stars•00 issues•00 pull requests•Updated Mar 6, 2024Mar 6, 2024

• computational_training

  Public
  Resources for computational training

  MIT License

  •00 forks•22 stars•00 issues•00 pull requests•Updated Jan 31, 2024Jan 31, 2024

• WaSP_simulations

  Public
  Repository for housing minimal reproducing scripts and chemical structures for water-soluble polymer (WaSP) MD studies

  Jupyter Notebook

  •

  MIT License

  •33 forks•00 stars•00 issues•00 pull requests•Updated Jan 26, 2024Jan 26, 2024

• glycoinsulin_analysis

  Public
  A python package for assessing the proteolytic stability and dimerization propensity of O-glycosylated insulin

  Python

  •00 forks•11 star•00 issues•00 pull requests•Updated Aug 22, 2023Aug 22, 2023

• cg_pyrosetta

  Public
  A python package which enables CG residues in a working version of PyRosetta

  Jupyter Notebook

  •

  MIT License

  •11 fork•66 stars•88 issues•22 pull requests•Updated Aug 16, 2023Aug 16, 2023

• TCPTP

  Public
  Analysis of MD Simulations of TCPTP

  Python

  •11 fork•00 stars•00 issues•00 pull requests•Updated Apr 17, 2023Apr 17, 2023

• alchemical_metadynamics_project

  Public
  Jupyter Notebook

  •22 forks•22 stars•00 issues•00 pull requests•Updated Feb 26, 2023Feb 26, 2023

• shirts_group_cbp_demo

  Public
  shirts_group_cbp_demo

  Python

  •

  MIT License

  •00 forks•00 stars•00 issues•00 pull requests•Updated Jan 19, 2023Jan 19, 2023

• cg_openmm

  Public
  Tools to build coarse grained models and perform simulations with OpenMM

  openmmcoarse-grained-molecular-dynamicsyank

  openmmcoarse-grained-molecular-dynamicsyank

  Python

  •

  MIT License

  •88 forks•2424 stars•6161 issues•33 pull requests•Updated Dec 16, 2022Dec 16, 2022

• OpenFFCrystalBenchmarking

  Public
  Jupyter Notebook

  •22 forks•11 star•55 issues•00 pull requests•Updated Oct 9, 2022Oct 9, 2022

• LLC_CG_build

  Public
  Python

  •22 forks•00 stars•00 issues•00 pull requests•Updated Sep 15, 2022Sep 15, 2022