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Commits on Dec 17, 2024

• Parse version from directory name if not a git repository. (#142)

  Show description for 0c1ae9b
  cgevans

  authored
  0c1ae9b

Commits on Dec 12, 2024

• Add a header to stress autocorrelation files

  lorenzo-rovigatti

  committed
  8036f9d

Commits on Dec 11, 2024

• fix documentation typo in oxDNA_PDB

  ErikPoppleton

  committed
  a66ce24

• update all forces converters to use the word 'forces' instead some using 'force'

  ErikPoppleton

  committed
  8c1060b

• Merge branch 'master' of https://github.com/lorenzo-rovigatti/oxDNA

  ErikPoppleton

  committed
  57ff94f

• Update dot-bracket utils to work with pseudoknots

  ErikPoppleton

  committed
  71e8c27

Commits on Nov 16, 2024

• Prepare the repo for the new release

  lorenzo-rovigatti

  committed
  b78d23c

• Fix a bug that made VMMC simulate the wrong model when used with the DNA2 interaction

  Show description for 6096fdb
  lorenzo-rovigatti

  committed
  6096fdb

Commits on Nov 15, 2024

• Fix a bug in the OXPY_REMD/reshuffle.py script, and strengthen the remd.py script

  lorenzo-rovigatti

  committed
  2ea602d

Commits on Nov 8, 2024

• Fix a bug whereby the code would hang if bases_file (used by HBEnergy) was not readable

  lorenzo-rovigatti

  committed
  a20df96

• Fix a stray debug print

  lorenzo-rovigatti

  committed
  e7c0d9e

Commits on Nov 4, 2024

• added PDB -> oxDNA to the docs

  ErikPoppleton

  committed
  7a9dd3e

• Added PDB -> oxDNA converter to oat

  ErikPoppleton

  committed
  e0084bc

Commits on Oct 31, 2024

• Make it possible to simulate LJ mixtures with attractive and repulsive interactions

  lorenzo-rovigatti

  committed
  3ad9bb7

Commits on Oct 30, 2024

• Fix #138: make oxpy's get_bool() to handle non-lowercase booleans (#139)

  Show description for 208049d
  elija-feigl

  authored
  208049d

Commits on Oct 25, 2024

• Make it possible to simulate arbitrary LJ binary mixtures

  lorenzo-rovigatti

  committed
  b191c3d

• Add to the docs a known issue referencing #137

  lorenzo-rovigatti

  committed
  f481eb4

Commits on Oct 23, 2024

• oat:faster linear version of decimate script / removing comments

  zoombya

  committed
  3bcd621

• oat:faster linear version of decimate script

  zoombya

  committed
  adbba3c

Commits on Oct 18, 2024

• ANNaMo: Fix the energy computation on GPU

  lorenzo-rovigatti

  committed
  d527509

• ANNaMo: add the possibility of using different interaction parameters for crossover beads

  lorenzo-rovigatti

  committed
  8ad9ce2

Commits on Oct 7, 2024

• Merge branch 'master' of https://github.com/lorenzo-rovigatti/oxDNA

  ErikPoppleton

  committed
  8ba1129

• fix parsing error for strand circularity in oat's new topology reader

  ErikPoppleton

  committed
  a168f8d

Commits on Sep 21, 2024

• Make the NA interaction support custom bases (fix #129)

  eryykr

  authored
  306a276

Commits on Sep 17, 2024

• Make it possible to print the kinetic and total energies with any precision

  lorenzo-rovigatti

  committed
  f42d61d

Commits on Sep 11, 2024

• Fixed bugs in pdb output file naming and improved RNA detection

  ErikPoppleton

  committed
  e753007

• Add more documentation (and debug output) related to cells_auto_optimisation (see #127)

  lorenzo-rovigatti

  committed
  51def37

Commits on Sep 9, 2024

• Add some documentation as a follow up to #122

  lorenzo-rovigatti

  committed
  ddc59c2

Commits on Sep 2, 2024

• Fix #123

  lorenzo-rovigatti

  committed
  f4853f9

Commits on Aug 30, 2024

• Fix #120

  Show description for 2b69edf
  lorenzo-rovigatti

  committed
  2b69edf

• Fix bug introduced in #113

  Show description for 68b8437
  lorenzo-rovigatti

  committed
  68b8437

Commits on Aug 29, 2024

• Added timing to the skeleton

  ErikPoppleton

  committed
  ca876ea

Commits on Aug 28, 2024

• added more detailed comments to bond_analysis

  ErikPoppleton

  committed
  6052b17

Commits on Aug 27, 2024

• Update oat API documentaiton

  ErikPoppleton

  committed
  32dbd3e

• Merge branch 'master' of https://github.com/lorenzo-rovigatti/oxDNA

  ErikPoppleton

  committed
  9a5bc1c

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