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@CCPBioSim

CCPBioSim

This is the development repository of the Collaborative Computational Project for Biomolecular Simulation

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  1. qmmm-workshop qmmm-workshop Public

    A repository containing the build steps for the ccpbiosim workshop on QM/MM

    Jupyter Notebook 70 21

  2. fesetup fesetup Public archive

    A tool for setting up free energy simulations.

    Python 37 18

  3. CCP5_Simulation_of_BioMolecules CCP5_Simulation_of_BioMolecules Public

    Jupyter Notebook 23 10

  4. mdanalysis-ml-workshop mdanalysis-ml-workshop Public

    Jupyter Notebook 17 5

  5. prepmd prepmd Public

    Automatically prepare structures from the PDB for molecular dynamics simulation

    Python 14 2

  6. biosim-analysis-workshop biosim-analysis-workshop Public

    Workshop on the preparation, execution, and analysis of protein molecular dynamics simulations

    Jupyter Notebook 12 4

Repositories

Showing 10 of 76 repositories
  • SIST Public

    SIST calculates stress-induced structural transition probabilities in superhelical DNA, including strand separation, Z-DNA formation, cruciform extrusion, and competition between these transitions.

    CCPBioSim/SIST's past year of commit activity
    C++ 2 MIT 0 16 1 Updated Sep 24, 2026
  • CodeEntropy Public

    Python package for calculating configurational entropy from molecular dynamics simulations using the multiscale cell correlation method.

    CCPBioSim/CodeEntropy's past year of commit activity
    Python 11 MIT 5 6 2 Updated Sep 24, 2026
  • biosim-schema Public

    Schema for biomolecular simulation metadata

    CCPBioSim/biosim-schema's past year of commit activity
    Python 0 MIT 0 2 1 Updated Sep 24, 2026
  • tw2026-coarse-graining-workshop Public Forked from chelsea-brown/Coarse-graining-workshop-2026
    CCPBioSim/tw2026-coarse-graining-workshop's past year of commit activity
    Jupyter Notebook 0 1 0 0 Updated Sep 24, 2026
  • tw2026-protein-simulation-workshop Public Forked from CCPBioSim/protein-simulation-workshop

    Workshop introducing simple MD simulations of a protein using Amber and OpenMM-based approaches

    CCPBioSim/tw2026-protein-simulation-workshop's past year of commit activity
    Jupyter Notebook 1 MIT 1 0 0 Updated Sep 24, 2026
  • qmmm-workshop Public

    A repository containing the build steps for the ccpbiosim workshop on QM/MM

    CCPBioSim/qmmm-workshop's past year of commit activity
    Jupyter Notebook 70 MIT 21 1 0 Updated Sep 23, 2026
  • ccpbiosim.github.io Public

    A developer facing web resource with various information and dashboards for the core ccpbiosim dev team

    CCPBioSim/ccpbiosim.github.io's past year of commit activity
    Python 2 MIT 1 7 1 Updated Sep 23, 2026
  • aiida-gromacs Public

    A GROMACS plugin for AiiDA

    CCPBioSim/aiida-gromacs's past year of commit activity
    Python 8 MIT 6 7 0 Updated Sep 23, 2026
  • aiida-amber Public

    An Amber plugin for AiiDA

    CCPBioSim/aiida-amber's past year of commit activity
    Python 2 MIT 3 5 0 Updated Sep 23, 2026
  • biosimdb-interface Public

    A web interface for extracting and uploading simulation metadata

    CCPBioSim/biosimdb-interface's past year of commit activity
    Python 0 MIT 0 2 0 Updated Sep 23, 2026
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