NERDSS v1.0

Initial Commit

• This repo is migrated from nerdss_development

What's Changed

• fixed loop_close issue when rates are high by @sikaoguo22 in #2
• changed output structure; now the outputs are categorized into DATA, PDB, and RESTARTS. Be aware that this is a breaking change where the old analyzer scripts might not work.
  (Commits in nerdss_development)
• Commits on Dec 17, 2025
  Add '_' underscore separator support to the BNGL parser
• Commits on Dec 1, 2025
  transition matrix typo
• transition matrix typo
• accept any 1D movement when overlap happens
• 1D reaction within the same complex still uses get_distance since Rmax is defined in aother way
• Correct reweighting for colocalized protein interacting with 1D sites
• fix segfault when using clusterOverlapCheck without implicit lipids

Changed by

• @sikaoguo22
• @sangmk
• @PhysFoley
• @yingyue2030699

Full Changelog: https://github.com/JohnsonBiophysicsLab/NERDSS/commits/v1.0