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Shirts Research Group

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  1. InterMol InterMol Public

    Conversion tool for molecular simulations

    Python 216 58

  2. physical_validation physical_validation Public

    Physical validation of molecular simulations

    Python 57 20

  3. cg_openmm cg_openmm Public

    Tools to build coarse grained models and perform simulations with OpenMM

    Python 25 8

  4. checkensemble checkensemble Public

    This software allows users to perform statistical test to determine if a given molecular simulation is consistent with the thermodynamic ensemble it is performed in.

    Python 14 8

  5. software-physical-validation software-physical-validation Public

    Best Practices article (intended for LiveCoMS) treating simulation software validation and physical validation

    TeX 9 2

  6. cg_pyrosetta cg_pyrosetta Public

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

    Jupyter Notebook 6 1

Repositories

Showing 10 of 61 repositories
  • terphenyl_simulations Public

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

    shirtsgroup/terphenyl_simulations’s past year of commit activity
    Jupyter Notebook 0 MIT 1 0 5 Updated Nov 25, 2025
  • pymbar_notebook_examples Public

    Notebooks of pymbar examples

    shirtsgroup/pymbar_notebook_examples’s past year of commit activity
    Jupyter Notebook 2 MIT 2 0 0 Updated Nov 14, 2025
  • physical_validation Public

    Physical validation of molecular simulations

    shirtsgroup/physical_validation’s past year of commit activity
    Python 57 MIT 20 12 5 Updated Oct 6, 2025
  • polymerist Public Forked from timbernat/polymerist

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

    shirtsgroup/polymerist’s past year of commit activity
    Python 1 MIT 4 0 0 Updated Sep 25, 2025
  • Shift_switch_free_energy Public Forked from lwhitm1/Shift_switch_free_energy
    shirtsgroup/Shift_switch_free_energy’s past year of commit activity
    Shell 0 MIT 1 0 0 Updated Jul 22, 2025
  • potatohead Public

    links for enhanced sampling papers and code

    shirtsgroup/potatohead’s past year of commit activity
    3 1 0 0 Updated Jul 14, 2025
  • FAS Public Forked from ajfriedman22/FAS

    Studying Fatty Acid Biosynthesis using Computational Methods

    shirtsgroup/FAS’s past year of commit activity
    MATLAB 0 MIT 2 0 0 Updated Jul 9, 2025
  • ensemble_md Public Forked from weitse-hsu/ensemble_md

    A python package for performing GROMACS simulation ensembles

    shirtsgroup/ensemble_md’s past year of commit activity
    Python 0 MIT 4 0 0 Updated Jul 6, 2025
  • Lipids_Best_Practices Public

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

    shirtsgroup/Lipids_Best_Practices’s past year of commit activity
    TeX 0 0 0 0 Updated Jun 7, 2025
  • solvation_shells Public Forked from schwinns/solvation_shells

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

    shirtsgroup/solvation_shells’s past year of commit activity
    Jupyter Notebook 1 1 0 0 Updated May 27, 2025
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