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@molmod Center for Molecular Modeling (CMM), Ghent University

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    28 repositories

    • acid

      Public
      The AutoCorrelation Integral Drill (ACID) -- Dataset
      pythonpsddataset
      pythonpsddatasetacfstepuptypstautocorrelation-functionworfklowsystematic-validationautocorrelation-integral
      Python
      •
      Creative Commons Attribution Share Alike 4.0 International
      •2•2•4•0•Updated Apr 15, 2026Apr 15, 2026

    • stacie

      Public
      Stable AutoCorrelation Integral Estimator
      open-sourcepsdmolecular-dynamics
      open-sourcepsdmolecular-dynamicsscientific-computingdata-analysisacfpost-processinguncertainty-quantificationlgplpython-package
      Python
      •
      GNU Lesser General Public License v3.0
      •6•17•1•0•Updated Apr 5, 2026Apr 5, 2026

    • psiflow

      Public
      scalable molecular simulation
      machine-learningdftmolecular-dynamics
      machine-learningdftmolecular-dynamicspytorchquantum-chemistrytransfer-learningcp2kenhanced-samplingcoupled-clusterfree-energy-calculations
      Python
      •
      MIT License
      •15•141•10•2•Updated Mar 30, 2026Mar 30, 2026

    • acid-test

      Public
      The AutoCorrelation Integral Drill (ACID) -- Test Bench
      pythonworkflowpsd
      pythonworkflowpsddatasetacfpower-spectral-densitystepuptypstautocorrelation-functionsystematic-validation
      Python
      •
      Creative Commons Attribution Share Alike 4.0 International
      •1•1•0•0•Updated Mar 30, 2026Mar 30, 2026

    • soapboxslide

      Public
      A Computational Soap Box Slide
      pythoneducationracing
      pythoneducationracingnumpyautogradscientific-computingmatplotlibsoapboxjax
      Python
      •
      GNU General Public License v3.0
      •0•2•0•0•Updated Mar 24, 2026Mar 24, 2026

    • openmm-tutorial-msbs

      Public
      OpenMM tutorial for the MSBS course
      education
      education
      Jupyter Notebook
      •50•189•3•0•Updated Mar 19, 2026Mar 19, 2026

    • optdesign

      Public
      Optimal Design (tutorial) with MaxVol algorithms
      Python
      •
      GNU Lesser General Public License v3.0
      •0•4•0•0•Updated Mar 19, 2026Mar 19, 2026

    • ThermoLIB

      Public
      ThermoLIB is a library for the construction, manipulation and post-processing of free energy surfaces from output of molecular simulations
      Jupyter Notebook
      •
      GNU General Public License v3.0
      •2•5•0•0•Updated Mar 11, 2026Mar 11, 2026

    • copacof

      Public
      Python
      •
      MIT License
      •2•0•0•1•Updated Feb 19, 2026Feb 19, 2026

    • chargedist

      Public
      Tutorial on charge equilibration, a.k.a electronegativity equalization
      Jupyter Notebook
      •
      Creative Commons Attribution Share Alike 4.0 International
      •0•2•0•0•Updated Dec 19, 2025Dec 19, 2025

    • tinyff

      Public
      Minimalistic force-field implementation for teaching purposes
      Python
      •
      GNU General Public License v3.0
      •0•6•0•0•Updated Oct 18, 2025Oct 18, 2025

    • sbc

      Public
      learned collective variables using smooth basin classification
      Python
      •
      MIT License
      •0•0•0•0•Updated Dec 22, 2024Dec 22, 2024

    • transfermace

      Public
      Reference implementation of the transfer learning approach from 10.26434/chemrxiv-2024-zg9v6
      Python
      •
      MIT License
      •0•4•0•0•Updated Oct 25, 2024Oct 25, 2024

    • molmod

      Public
      MolMod is a collection of molecular modelling tools for python.
      Python
      •
      GNU General Public License v3.0
      •23•60•8•3•Updated Feb 21, 2024Feb 21, 2024

    • QuantumCourses

      Public
      Quantum mechanics related courses taught by the CMM
      Jupyter Notebook
      •4•1•0•0•Updated Nov 24, 2023Nov 24, 2023

    • tamkin

      Public
      TAMkin is a post-processing toolkit for thermochemistry and kinetics analysis.
      Python
      •
      GNU General Public License v3.0
      •15•23•8•3•Updated Nov 20, 2023Nov 20, 2023

    • QuickFF

      Public
      A Python code to quickly derive ab initio parameterized force fields.
      Python
      •
      GNU General Public License v3.0
      •15•44•7•1•Updated Nov 7, 2023Nov 7, 2023

    • pyiron

      Public
      pyiron - an integrated development environment (IDE) for computational materials science.
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •55•0•0•0•Updated Sep 28, 2023Sep 28, 2023

    • micmec

      Public
      MicMec, the first implementation of the micromechanical model, ever.
      simulationmolecular-dynamicscoarse-graining
      simulationmolecular-dynamicscoarse-grainingmetal-organic-frameworks
      Python
      •
      GNU General Public License v3.0
      •0•6•0•0•Updated Aug 24, 2023Aug 24, 2023

    • gpxrdpy

      Public
      Python wrapper for PXRD pattern calculation based on pyobjcryst
      Python
      •
      GNU General Public License v3.0
      •1•4•0•0•Updated Aug 22, 2023Aug 22, 2023

    • md-tracks

      Public archive
      MD-Tracks is a statistical analysis toolkit for molecular dynamics and monte carlo simulations.
      Python
      •
      GNU General Public License v3.0
      •2•9•0•0•Updated Apr 14, 2023Apr 14, 2023

    • hipart

      Public archive
      HiPart is a program to analyze the electronic structure of molecules with fuzzy-atom partitioning methods.
      Python
      •
      GNU General Public License v3.0
      •3•2•0•0•Updated Apr 14, 2023Apr 14, 2023

    • pysqa

      Public
      Simple queue adapter for Python
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •8•0•0•0•Updated Nov 7, 2022Nov 7, 2022

    • pyiron-resources

      Public
      Resource folder for pyiron - an integrated development environment (IDE) for computational materials science.
      Forth
      •6•0•0•0•Updated Oct 19, 2022Oct 19, 2022

    • yaff

      Public
      Yaff is yet another force-field code
      Python
      •
      GNU General Public License v3.0
      •18•38•4•0•Updated Oct 6, 2022Oct 6, 2022

    • Tutorial

      Public
      IPython tutorial notebooks for master students
      Jupyter Notebook
      •8•3•0•0•Updated Sep 13, 2021Sep 13, 2021

    • DeltaCodesDFT

      Public
      Scripts needed to generate the Delta factor for two solid state DFT codes within the PBE formalism
      Python
      •
      GNU Lesser General Public License v2.1
      •5•9•1•0•Updated Apr 28, 2020Apr 28, 2020

    • zeobuilder

      Public
      Zeobuilder is an extensible GUI-toolkit for molecular model construction.
      Python
      •
      GNU General Public License v3.0
      •10•13•0•0•Updated Feb 15, 2019Feb 15, 2019
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