Issues

• mBuild and MDAnalysis exporters put coarse-grained beads in different places (centroid vs. center of mass)

  MuPT-hub/mupt#169 · Filter by author joelaforet opened on Nov 12, 2026
  2

• Exported atoms need hierarchy (depth-first) order: breadth-first cross_section splits residues in PDB, OpenMM and GROMACS output

  MuPT-hub/mupt#163 · Filter by author joelaforet opened on Nov 4, 2026
  2

  

• How to build an all-atom system from SMILES using the new API? (blocking a MuPT → flowerMD AA-DPD example)

  MuPT-hub/mupt#156 · Filter by author joelaforet opened on Nov 3, 2026
  2

  

• Simplify complex logic throughout codebase

  developmentinternalMuPT 2.0
  MuPT-hub/mupt#146 · Filter by author timbernat opened on Oct 30, 2026

• Replace signature calls for networkx drawing keywords with explicitly-named arguments

  developmentinternal
  Task

  MuPT-hub/mupt#145 · Filter by author timbernat opened on Oct 29, 2026
  

• Reconnect AA-DPD builder to use mupt_to_mbuild [stub]

  MuPT-hub/mupt#139 · Filter by author mrshirts opened on Oct 22, 2026
  3

  

• Planning coordinate builders and interfaces for post-1.0 [draft - MRS still sketching out]

  geometryinterfaceMuPT 2.0
  MuPT-hub/mupt#138 · Filter by author mrshirts opened on Oct 22, 2026

• Self-avoiding random-walks

  MuPT-hub/mupt#137 · Filter by author ggolde opened on Oct 21, 2026

• MuPT Interface to Freud (in addition to the MDAnalysis interface)

  analysisenhancementMuPT 2.0
  MuPT-hub/mupt#129 · Filter by author joelaforet opened on Oct 14, 2026

• has_SAAMR_roles only checks role presence, not SAAMR arrangement

  MuPT-hub/mupt#127 · Filter by author joelaforet opened on Oct 12, 2026
  

• OOP high-level API ideas

  enhancementuser-interface
  MuPT-hub/mupt#117 · Filter by author ggolde opened on Sep 24, 2026
  1

• Stereochemistry is not preserved during AA-DPD initialization

  bugchemistryMuPT 1.0
  Bug

  MuPT-hub/mupt#116 · Filter by author joelaforet opened on Sep 24, 2026 · MuPT 1.0
  

• Polymer melt initialization

  MuPT-hub/mupt#115 · Filter by author jnnsmpth opened on Sep 24, 2026
  

• Going from MuPT -> OpenFF Interchange

  MuPT-hub/mupt#110 · Filter by author joelaforet opened on Sep 10, 2026
  1

  

• Exporting 1-bead/repeat_unit CG representations to MDAnalysis

  analysisMuPT 1.0
  Feature

  MuPT-hub/mupt#109 · Filter by author joelaforet opened on Sep 10, 2026 · MuPT 1.0
  

• Make it so docs are available of docs.mupt.org

  documentation
  MuPT-hub/mupt#108 · Filter by author dwhswenson opened on Sep 10, 2026

• Docs: Developing

  documentation
  MuPT-hub/mupt#107 · Filter by author dwhswenson opened on Sep 10, 2026

• Docs: Getting Started

  documentation
  MuPT-hub/mupt#106 · Filter by author dwhswenson opened on Sep 10, 2026

• Docs: Tutorials vs. How-Tos in the Examples

  documentation
  MuPT-hub/mupt#105 · Filter by author dwhswenson opened on Sep 10, 2026

• Explanation Doc: Getting to 3D

  documentation
  MuPT-hub/mupt#104 · Filter by author dwhswenson opened on Sep 10, 2026

• Explanation Doc: Connectors

  documentation
  MuPT-hub/mupt#102 · Filter by author dwhswenson opened on Sep 10, 2026
  

• Explanation Doc: Representation/Topology

  documentation
  MuPT-hub/mupt#101 · Filter by author dwhswenson opened on Sep 10, 2026
  

• Clarification of how CG-DPD gets particle sizes

  MuPT-hub/mupt#88 · Filter by author mrshirts opened on Jun 26, 2026
  

• Create easier convenience functions, interfaces for initializing a system

  MuPT-hub/mupt#85 · Filter by author mrshirts opened on Jun 18, 2026
  7

  

• Add Unified YAML Configuration Support for REACTER and PolymerizeIt!

  enhancement
  Feature

  MuPT-hub/mupt#84 · Filter by author janitha-mahanthe opened on Jun 18, 2026
  4