OpenBioSim/sire

Issues

• [BUG] Sire OpenMM context minimiser isn't thread safe

  #259 opened 24 days ago by lohedges
  8

• Definition of force constants inconsistent between Boresch restraints correction and applied restraints

  #248 opened a month ago by fjclark
  2

• [BUG] dynamic.minimise() is missing timeout kwarg

  #253 opened a month ago by lohedges
  0

• [BUG] Inconsistent behaviour of dynamics.minimise and system.minimisation

  #255 opened a month ago by lohedges
  5

• [BUG] Frames and energies are always saved after dynamics.run()

  #256 opened a month ago by lohedges
  2

• [BUG] Sire::Mol::Frame::toByteArray initialises QByteArray incorrectly

  #249 opened a month ago by lohedges
  0

• [BUG] CacheData::cleanUpOnExit kills QThread objects too quickly

  #251 opened a month ago by lohedges
  0

• [BUG] Trajectories are not properly stored after `mols.delete_all_frames()` is called.

  #218 opened 4 months ago by mb2055
  16

• Definition of Annihilation

  #245 opened a month ago by fjclark
  3

• [BUG] Constraints in OpenMM context aren't updated

  #244 opened a month ago by lohedges
  0

• [BUG] Minimisation/Dynamics failing when using positional restraints

  #232 opened 2 months ago by mb2055
  0

• [BUG] self._omm_state isn't set to None after minimisation

  #242 opened 2 months ago by lohedges
  0

• [BUG] Minimiser hangs

  #230 opened 2 months ago by lohedges
  3

• [BUG] Replica exchange fails in NPT ensemble

  #234 opened 2 months ago by mb2055
  0

• [BUG] to/from ghost interactions aren't excluded from the ghost_14 force field

  #239 opened 2 months ago by lohedges
  0

• [BUG] Incorrect delta energy evaluated following constraint projection after energy minimisation

  #241 opened 2 months ago by lohedges
  0

• [BUG] Buffer overflow causes inconsistent number of ghost-ghost exclusions

  #236 opened 2 months ago by lohedges
  0

• [BUG] Incorrect calculation of soft-core Coulomb delta parameter

  #238 opened 2 months ago by lohedges
  0

• [BUG] Asymmetric exclusions for ghost-ghost interactions

  #240 opened 2 months ago by lohedges
  4

• debug mode for alchemical trajectory analyses

  #231 opened 2 months ago by jmichel80
  0

• [BUG] Issues with dummy atomtypes in perturbable GROMACS topologies

  #228 opened 3 months ago by lohedges
  0

• [BUG] Issue with the approach described to combine EMLE and OpenMM-ML

  #227 opened 3 months ago by JMorado
  5

• [BUG] GroTop parser doesn't read water bond and angle terms within #ifdef FLEXIBLE block

  #224 opened 4 months ago by noahharrison64
  8

• Migrate rdkit-dev to librdkit-dev

  #217 opened 4 months ago by skearnes
  12

• [BUG] IFBOX pointer not set correctly for triclinic boxes

  #215 opened 4 months ago by CHENFENG1020
  9

• [BUG] OpenMMPMEFep wrappers aren't excluded when OpenMM is missing

  #213 opened 4 months ago by lohedges
  1

• [BUG] Undesired behaviour in systems with multiple perturbable molecules

  #219 opened 4 months ago by mb2055
  0

• [BUG] SOMD "charge difference" option only works from the command-line

  #212 opened 4 months ago by lohedges
  0

• Improve logging of co-alchemical water perturbations in SOMD1

  #208 opened 5 months ago by jmichel80
  1

• [BUG] Inconsistent behaviour with reindexed molecules

  #202 opened 5 months ago by lohedges
  6

• [BUG] make_whole center kwarg not exposed

  #199 opened 5 months ago by lohedges
  1

• Add trajectory sorting function

  #191 opened 7 months ago by chryswoods
  0

• Add support for reading Gromacs FEP topology files

  #169 opened 9 months ago by chryswoods
  2

• [BUG] Update cmake version as upcoming deprecation

  #184 opened 8 months ago by chryswoods
  2

• [BUG] mol.move().align() fails to align two proteins

  #192 opened 5 months ago by akalpokas
  3

• [BUG] somd-freenrg is expanding the water box

  #203 opened 5 months ago by nigel-palmer-cresset
  9

• GROMACS host requirement is breaking macOS CI

  #193 opened 5 months ago by lohedges
  4

• [BUG] RDKit pin isn't strict enough

  #200 opened 5 months ago by lohedges
  0

• [BUG] GroTop parser fails when position restraint include directives are present

  #194 opened 6 months ago by lohedges
  2

• [BUG] somd-freenrg.py fails with "Periodic box vectors must be in reduced form"

  #197 opened 6 months ago by nigel-palmer-cresset
  5

• [BUG] AttributeError: 'EMLEEngine' object has no attribute 'get_forces'

  #196 opened 6 months ago by Lactoria-cornuta
  4

• [BUG] ForceFieldInfo sets incorrect cutoff from a TriclinicBox space

  #189 opened 7 months ago by Lactoria-cornuta
  8

• [BUG] sire.morph.create_from_pertfile doesn't assign different element properties to the end states

  #186 opened 7 months ago by lohedges
  0

• Add square root, power etc to units

  #176 opened 8 months ago by chryswoods
  2

• Add "auto" constraints and then update tutorial

  #185 opened 8 months ago by chryswoods
  1

• Preserve PDB information when interconverting with RDKit

  #168 opened 8 months ago by chryswoods
  0

• [BUG] create_from_pertfile uses next instead of continue when skipping atoms that don't match the perturbation template

  #179 opened 8 months ago by lohedges
  2

• Not recognising amide bond?

  #177 opened 8 months ago by chryswoods
  1

• [BUG] - Iron not recognised as a biological element

  #170 opened 9 months ago by chryswoods
  0

• [BUG] Mol2 parser element inference isn't robust

  #166 opened 9 months ago by lohedges
  0