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    21 repositories

    • polyply_1.0

      Public
      Generate input parameters and coordinates for atomistic and coarse-grained simulations of polymers, ssDNA, and carbohydrates
      dnahacktoberfestatomistic-simulations
      dnahacktoberfestatomistic-simulationsmdmartinicarbohydratescoarse-grainingpolymersmacromolecules
      Python
      •
      Apache License 2.0
      •37•199•50•15•Updated Sep 11, 2026Sep 11, 2026

    • vermouth-martinize

      Public
      Describe and apply transformation on molecular structures and topologies
      molecular-dynamicshacktoberfest
      molecular-dynamicshacktoberfest
      Python
      •
      Apache License 2.0
      •61•150•140•19•Updated Sep 9, 2026Sep 9, 2026

    • metabolite-cytosol-paper

      Public
      Code for figures for the Martini 3 cytosol paper
      Python
      •0•0•0•0•Updated Aug 18, 2026Aug 18, 2026

    • bentopy

      Public
      Packs stuff in boxes
      molecular-dynamicsmartinicomputational-biophysics
      molecular-dynamicsmartinicomputational-biophysics
      Rust
      •
      Other
      •2•25•2•0•Updated Jul 7, 2026Jul 7, 2026

    • TS2CG1.1

      Public
      TS2CG version 1.1
      C++
      •4•8•4•1•Updated Jan 13, 2026Jan 13, 2026

    • MDVoxelSegmentation

      Public
      A voxel based approach for dynamic cluster analysis of molecular dynamics trajectories.
      HTML
      •
      Other
      •12•34•15•0•Updated Nov 5, 2025Nov 5, 2025

    • martinize-examples

      Public
      Examples for Martinize2 and vermouth
      Python
      •
      Apache License 2.0
      •0•2•1•0•Updated Oct 23, 2025Oct 23, 2025

    • TS2CG

      Public
      TS2CG: Conversion of triangulated surfaces to (coarse grain) membrane models for molecular simulation
      HiveQL
      •
      Apache License 2.0
      •7•31•3•0•Updated Apr 17, 2025Apr 17, 2025

    • martini-workshop

      Public
      Martini Workshop: Simulating a Minimal Bacterial Cell
      Tcl
      •4•18•3•1•Updated May 13, 2024May 13, 2024

    • shocker

      Public
      Setting up and running simulations imitating the process of osmotic shocking
      Python
      •
      Apache License 2.0
      •0•7•4•1•Updated Dec 10, 2023Dec 10, 2023

    • polyply_regression_tests

      Public
      Regression tests and tutorial input files for the polyply software suite
      Python
      •
      Apache License 2.0
      •3•1•0•0•Updated Jun 24, 2023Jun 24, 2023

    • martini-forcefields

      Public
      Collection of interaction and molecule parameters for the Martini3 force-field
      Python
      •
      Apache License 2.0
      •6•23•1•1•Updated Feb 7, 2023Feb 7, 2023

    • Martini_Minimal_Cell

      Public
      2•8•1•0•Updated Jan 16, 2023Jan 16, 2023

    • PEGylated_proteins_tutorial

      Public
      Files required for our tutorial on PEGylated proteins
      tutorialcoarse-grainedmd
      tutorialcoarse-grainedmdpegylated-proteins
      Tcl
      •0•3•0•0•Updated Aug 30, 2022Aug 30, 2022

    • VisualizationServer

      Public
      Managing all issues and suggestions regarding the Visualization Server. This tracking is meant for issues raised by users both inside the Molecular Dynamics gro…
      0•1•3•0•Updated Apr 6, 2022Apr 6, 2022

    • martini_sour

      Public
      Setup and run titratable Martini simulations
      Python
      •
      Apache License 2.0
      •0•2•10•1•Updated Dec 5, 2021Dec 5, 2021

    • martini_sour_examples

      Public
      Examples corresponding to marrink-lab/martini_sour
      Shell
      •
      Apache License 2.0
      •0•1•0•0•Updated Dec 5, 2021Dec 5, 2021

    • gromit

      Public
      Auxiliary tools for automated atomistic and coarse-grained molecular dynamics simulations using gromacs
      Python
      •
      GNU General Public License v2.0
      •12•11•8•1•Updated Apr 23, 2021Apr 23, 2021

    • pycgbuilder

      Public
      A Qt5 based GUI for making mapping files
      Python
      •
      Apache License 2.0
      •1•3•2•0•Updated Nov 20, 2020Nov 20, 2020

    • cgbuilder

      Public
      Build coarse-grained mapping for molecules from a web-GUI
      JavaScript
      •
      Apache License 2.0
      •5•0•0•0•Updated Dec 12, 2018Dec 12, 2018

    • cartographer

      Public
      Python
      •
      Apache License 2.0
      •2•9•0•0•Updated Jul 17, 2018Jul 17, 2018
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