OpenFreeEnergy/openfe-benchmarks

Issues

• Charge correction: investigate other systems?

  #38 opened a year ago by hannahbaumann
  1

• Charge correction: run a larger CDK2 radial network

  #37 opened a year ago by hannahbaumann
  1

• Charge correction: investigate ion concentration?

  #36 opened a year ago by hannahbaumann
  1

• Charge correction: effect of box size?

  #35 opened a year ago by hannahbaumann
  1

• Consistency test for RFE charge correction

  #34 opened a year ago by hannahbaumann
  0

• Charge correction: longer simulations of CDK2?

  #33 opened a year ago by hannahbaumann
  2

• Kartograf mapper, Lomap network, no element changes

  #32 opened a year ago by hannahbaumann
  1

• Kartograf MST, element changes, openfe 0.14

  #31 opened a year ago by hannahbaumann
  1

• Kartograf MST, no element changes, openfe 0.14

  #30 opened a year ago by hannahbaumann
  1

• Benchmark manually curated edges [Ken's edges]

  #17 opened a year ago by IAlibay
  0

• Prune bad edges from redundant networks

  #29 opened a year ago by IAlibay
  0

• [Kartograf mapper, Lomap scorer, Lomap network] benchmark

  #14 opened a year ago by IAlibay
  3

• [Lomap mapper, Lomap scorer, Lomap Network] benchmark

  #25 opened a year ago by IAlibay
  1

• [Perses mapper, Perses scorer, MST network (after sign flip correction)] benchmark

  #22 opened a year ago by hannahbaumann
  4

• [Lomap mapper, Lomap scorer, radial network] benchmark

  #13 opened a year ago by IAlibay
  1

• [Kartograf mapper, Lomap Scorer, MST network] benchmark

  #10 opened a year ago by IAlibay
  1

• [Lomap mapper, Lomap scorer, MST network] benchmark

  #9 opened a year ago by IAlibay
  1

• HiMap network [Lomap mapper, Lomap scorer] for tyk2, ptp1b, shp2 using 1/3 of sim time

  #24 opened a year ago by hannahbaumann
  1

• Radial Network [Kartograf, smallest ligand center]

  #26 opened a year ago by IAlibay
  0

• HiMap network [Lomap mapper, Lomap scorer] for tyk2, ptp1b, shp2

  #23 opened a year ago by hannahbaumann
  0

• Very short simulation benchmarks [Kartograf mapper, Lomap scorer, MST]

  #19 opened a year ago by IAlibay
  0

• HiMap networks w/ early termination

  #20 opened a year ago by IAlibay
  0

• Non-equilibrium cycling benchmarks

  #21 opened a year ago by IAlibay
  0

• Add historical OpenFF 2.1 vs 2.0 benchmarking results

  #18 opened a year ago by IAlibay
  0

• Add Perses MST benchmarks

  #11 opened a year ago by IAlibay
  0

• Add perses star map data

  #8 opened a year ago by IAlibay
  0

• HiMap network benchmarks [Kartograf, Lomap scorer, n*ln(n) edges]

  #16 opened a year ago by IAlibay
  0

• HiMap network [Kartograf mapper, Lomap scorer, Lomap edge number]

  #15 opened a year ago by IAlibay
  0

• Add Perses MST benchmark with Lomap scorer

  #12 opened a year ago by IAlibay
  0

• Give the option to read mappings from file & maybe also the connections table

  #4 opened 2 years ago by IAlibay
  0

• Squash tests using parametrize

  #3 opened 2 years ago by IAlibay
  0

• Investigate duplicate numbered residue in thrombin PDB

  #2 opened 2 years ago by IAlibay
  0

• Update README

  #1 opened 3 years ago by IAlibay
  0