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    61 repositories

    • terphenyl_simulations

      Public
      Repository for storing simulation input files and analysis code for terphenyl simulations
      Jupyter Notebook
      •
      MIT License
      •1•0•0•5•Updated Jul 22, 2025Jul 22, 2025

    • pymbar_notebook_examples

      Public
      Notebooks of pymbar examples
      Jupyter Notebook
      •
      MIT License
      •1•2•0•0•Updated Jul 22, 2025Jul 22, 2025

    • Shift_switch_free_energy

      Public
      Shell
      •
      MIT License
      •1•0•0•0•Updated Jul 22, 2025Jul 22, 2025

    • potatohead

      Public
      links for enhanced sampling papers and code
      0•1•0•0•Updated Jul 14, 2025Jul 14, 2025

    • FAS

      Public
      Studying Fatty Acid Biosynthesis using Computational Methods
      MATLAB
      •
      MIT License
      •2•0•0•0•Updated Jul 9, 2025Jul 9, 2025

    • physical_validation

      Public
      Physical validation of molecular simulations
      pythonmolecular-dynamicsmolecular-simulationmolecular-mechanicsphysical-validation
      Python
      •
      MIT License
      •20•56•12•5•Updated Jul 7, 2025Jul 7, 2025

    • ensemble_md

      Public
      A python package for performing GROMACS simulation ensembles
      Python
      •
      MIT License
      •4•0•0•0•Updated Jul 6, 2025Jul 6, 2025

    • Lipids_Best_Practices

      Public
      A description of best practices for fitting lipid force fields to experiments
      TeX
      •0•0•0•0•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
      •1•0•0•0•Updated May 27, 2025May 27, 2025

    • polymerist

      Public
      Polymer-Oriented LibrarY of Monomer-Expression Rules and In-silico Synthesis Tools
      Python
      •
      MIT License
      •3•1•0•0•Updated Jan 25, 2025Jan 25, 2025

    • scalems_optimizedg

      Public
      Files for test of optimizing dg
      Jupyter Notebook
      •
      MIT License
      •0•0•0•0•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
      •1•2•0•0•Updated Sep 25, 2024Sep 25, 2024

    • openff_examples

      Public
      Example notebooks for carrying out various OpenFF tasks
      Jupyter Notebook
      •
      MIT License
      •0•1•0•0•Updated Sep 4, 2024Sep 4, 2024

    • alchemistry.org

      Public
      Source for alchemistry.org web page
      Jupyter Notebook
      •
      Other
      •0•0•0•0•Updated Sep 3, 2024Sep 3, 2024

    • OpenFF_Bilayer

      Public
      Jupyter Notebook
      •3•0•0•0•Updated Aug 29, 2024Aug 29, 2024

    • eyring_model

      Public
      Jupyter Notebook
      •1•0•0•0•Updated Aug 26, 2024Aug 26, 2024

    • InterMol

      Public
      Conversion tool for molecular simulations
      Python
      •
      MIT License
      •57•210•86•6•Updated Jun 12, 2024Jun 12, 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 design"
      Python
      •
      MIT License
      •0•0•0•0•Updated Mar 22, 2024Mar 22, 2024

    • simulation_essentials

      Public
      GitHub repository for lessons on simulations
      Jupyter Notebook
      •
      MIT License
      •0•0•0•0•Updated Mar 6, 2024Mar 6, 2024

    • NMRLipidsDatabankCode

      Public
      NMRlipids databank with altered code for local analysis
      Jupyter Notebook
      •
      GNU General Public License v3.0
      •33•0•0•0•Updated Mar 6, 2024Mar 6, 2024

    • computational_training

      Public
      Resources for computational training
      MIT License
      •0•2•0•0•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
      •2•0•0•0•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
      •0•1•0•0•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
      •1•6•8•2•Updated Aug 16, 2023Aug 16, 2023

    • TCPTP

      Public
      Analysis of MD Simulations of TCPTP
      Python
      •1•0•0•0•Updated Apr 17, 2023Apr 17, 2023

    • alchemical_metadynamics_project

      Public
      Jupyter Notebook
      •2•2•0•0•Updated Feb 26, 2023Feb 26, 2023

    • shirts_group_cbp_demo

      Public
      shirts_group_cbp_demo
      Python
      •
      MIT License
      •0•0•0•0•Updated Jan 19, 2023Jan 19, 2023

    • cg_openmm

      Public
      Tools to build coarse grained models and perform simulations with OpenMM
      openmmcoarse-grained-molecular-dynamicsyank
      Python
      •
      MIT License
      •8•24•61•3•Updated Dec 16, 2022Dec 16, 2022

    • OpenFFCrystalBenchmarking

      Public
      Jupyter Notebook
      •2•1•5•0•Updated Oct 9, 2022Oct 9, 2022

    • LLC_CG_build

      Public
      Python
      •2•0•0•0•Updated Sep 15, 2022Sep 15, 2022