Issues

• Use Spectra/Eigen as a replacement for ARPACK

  APIWork in Progress
  Amber-MD/cpptraj#1162 · Filter by author drroe opened on Feb 12, 2026
  

• Integrating MDANCE functionality in CPPTRAJ

  Amber-MD/cpptraj#1161 · Filter by author ramirandaq opened on Feb 11, 2026
  2

• Regarding Minor/Major groove width analysis with base-pair number

  question
  Amber-MD/cpptraj#1145 · Filter by author SoumyaCYZ opened on Aug 1, 2025
  9

  

• Interface preparforleap with modXNA

  enhancementhelp wanted
  Amber-MD/cpptraj#1133 · Filter by author drroe opened on Mar 7, 2025
  

• Shift in grid-based calculations

  Amber-MD/cpptraj#1127 · Filter by author choutkaj opened on Jan 9, 2025
  6

• How best to handle cpptraj vs. cpptraj.{MPI,OMP,cuda}

  Amber-MD/cpptraj#1123 · Filter by author dacase opened on Dec 26, 2024
  5

• Regarding the Principal component analysis with CPPTRAJ

  bug
  Amber-MD/cpptraj#1122 · Filter by author satyajitkhatua09 opened on Dec 21, 2024
  4

  

• Create a conda package

  Amber-MD/cpptraj#1120 · Filter by author drroe opened on Dec 19, 2024
  18

  

• Cumulative radial distribution function

  Amber-MD/cpptraj#1107 · Filter by author Saqlain5565 opened on Oct 18, 2024

• Should multidihedral allow pseudo dihedrals?

  Feature Request
  Amber-MD/cpptraj#1097 · Filter by author drroe opened on Aug 16, 2024
  

• Creating mass-weighted covariance matrix

  question
  Amber-MD/cpptraj#1095 · Filter by author fatih4534 opened on Jul 21, 2024
  3

• lDDT measure

  Amber-MD/cpptraj#1084 · Filter by author rodrigogalindo opened on May 28, 2024

• K-means++ Style initialization

  Amber-MD/cpptraj#1078 · Filter by author drroe opened on May 2, 2024
  

• Adding Clustering via Extended Similarity Metrics

  Feature Request
  Amber-MD/cpptraj#1049 · Filter by author drroe opened on Sep 13, 2023
  5

• Distribution of the tetrahedral order parameter Q for TIP4P/2005

  Amber-MD/cpptraj#1044 · Filter by author Saqlain5565 opened on Aug 16, 2023

• Local structure index of water (LSI) code issue

  Amber-MD/cpptraj#1043 · Filter by author Saqlain5565 opened on Aug 3, 2023
  3

• NAStruct feature request: output axes info for bases and basepairs

  enhancementNew keywords
  Amber-MD/cpptraj#1036 · Filter by author tcbishop opened on Jul 8, 2023
  8

  

• GIST Should have the option to write binary files

  Feature Request
  Amber-MD/cpptraj#1024 · Filter by author drroe opened on Apr 6, 2023
  

• new macos issue

  Amber-MD/cpptraj#1020 · Filter by author hainm opened on Mar 10, 2023
  6

• NetCDF4/HDF5 issues to be addressed

  Amber-MD/cpptraj#1000 · Filter by author drroe opened on Nov 17, 2022
  

• Is reference to bulk water energetics done automatically in CPPTRAJ GIST?

  Amber-MD/cpptraj#998 · Filter by author noahharrison64 opened on Nov 16, 2022
  3

• To undergo GIST analysis can I fit my protein to a reference structure rather than apply strong position restraints?

  question
  Amber-MD/cpptraj#991 · Filter by author noahharrison64 opened on Sep 21, 2022
  3

• requesting utility enhancement--calculate volume of a binding site

  Amber-MD/cpptraj#977 · Filter by author ghost opened on Jun 27, 2022

• Checking NetCDF: Checking for bundled NetCDF: Should CPPTRAJ attempt to build its own netcdf? {y|n}: n

  Amber-MD/cpptraj#976 · Filter by author hainm opened on Jun 24, 2022
  1

• add a "range360" keyword to phipsi analysis of Amber20

  Amber-MD/cpptraj#925 · Filter by author qfyu opened on Dec 2, 2021