michellab/BioSimSpace

Issues

• Issue in reproducing the funnel methadynamics tutorial

  #428 opened a year ago by velocirraptor23
  2

• [BUG] Water molecule coordinates are setting to (0,0,0)

  #427 opened a year ago by ale94mleon
  4

• [BUG]

  #425 opened 2 years ago by jasmin-guven
  10

• Reporting a vulnerability

  #426 opened 2 years ago by igibek
  0

• Specify disulfide bridges during parameter file generation

  #368 opened 2 years ago by cespos
  39

• AnalysisError: SOMD free-energy analysis failed!

  #422 opened 2 years ago by velocirraptor23
  5

• A protein-ligand system for testing

  #324 opened 2 years ago by xiki-tempula
  4

• Add extra arguments to some functions

  #372 opened 2 years ago by cespos
  3

• Strategy for migration to OpenBioSim GitHub organisation

  #393 opened 2 years ago by lohedges
  1

• [BUG] Cannot import BioSimSpace after installation of biosimspace 2023.1.2 using mamba

  #421 opened 2 years ago by cespos
  3

• [BUG] OSError "It looks like you failed to include a topology file." when reading SDF which doesn't contain redundant bond order information

  #419 opened 2 years ago by noahharrison64
  10

• Are atomtypes meant to be updated when using repartitionHydrogenMass?

  #418 opened 2 years ago by noahharrison64
  16

• Unable to import BioSimSpace after mamba installation

  #410 opened 2 years ago by akalpokas
  12

• `_toRegularMolecule` failing with `convert_amber_dummies=True`

  #413 opened 2 years ago by msuruzhon
  15

• Pickling a parametrised molecule from an SDF file with GAFF2

  #415 opened 2 years ago by msuruzhon
  4

• Absolute Binding Free Energy Calculations with GROMACS

  #414 opened 2 years ago by fjclark
  7

• BioSimSpace.Align.viewMapping: py3Dmol.view not rendering in Jupyter Notebook

  #412 opened 2 years ago by lohedges
  11

• Would it be possible to include HiMap as an alternative to LoMap in the generateNetwork method?

  #409 opened 2 years ago by DreamCykl
  2

• Make _removeDummies() recognise dummy bonds

  #407 opened 2 years ago by msuruzhon
  10

• Making HMR work with dummies

  #405 opened 2 years ago by msuruzhon
  11

• OpenFF and AmberTools

  #384 opened 2 years ago by lohedges
  14

• Problem when converting Gro/Top to Rst7

  #404 opened 2 years ago by msuruzhon
  12

• Is it possible to add ions to an already solvated system, without adding any more water molecules?

  #400 opened 2 years ago by aniketsh
  4

• HILLS file not updating during restarting simulation

  #396 opened 2 years ago by rubinanoor9
  4

• Storage quota exceeded on the Anaconda cloud

  #395 opened 2 years ago by lohedges
  1

• 'BioSimSpace._SireWrappers.System' can only contain unique molecules.

  #386 opened 2 years ago by kexul
  8

• Specify ions during system setup

  #369 opened 2 years ago by cespos
  15

• Correction for funnel metadynamics

  #392 opened 2 years ago by guidsari
  3

• Inconsistent Reporting of Dihedral Energies

  #391 opened 2 years ago by fjclark
  5

• UnboundLocalError when loading Chamber topology file.

  #390 opened 2 years ago by TENeary
  2

• Paramaterising with openff issues

  #389 opened 2 years ago by annamherz
  13

• BioSimSpace.IO.readMolecules failed to read amber prm7 and rst7 file

  #387 opened 2 years ago by Naf-Guo
  2

• CI hangs / timeouts

  #385 opened 2 years ago by lohedges
  1

• The correct way of setting up the env for BSS for CI

  #383 opened 2 years ago by xiki-tempula
  25

• Exposing mapping from merged molecule to parent molecules

  #375 opened 2 years ago by kexul
  2

• Coupling groups in Gromacs

  #377 opened 2 years ago by cespos
  2

• Custom expression evaluation for steered Molecular Dynamics

  #362 opened 2 years ago by AdeleHardie
  3

• Align.viewMapping bug?

  #364 opened 2 years ago by ZCLIU-2022
  1

• Poor pickling performance on macOS

  #360 opened 2 years ago by lohedges
  3

• Improve interoperablilty of MDTraj/MDAnalysis trajectory handling

  #340 opened 2 years ago by xiki-tempula
  6

• Modify part of molecule's coordinate

  #350 opened 2 years ago by kexul
  3

• LOMAP fails with "AlignmentError: Unable to compute MCS of molecules!"

  #348 opened 2 years ago by jasmin-guven
  33

• __contain__ cannot handle protein

  #333 opened 2 years ago by xiki-tempula
  12

• Bug in updateMolecule()

  #343 opened 2 years ago by msuruzhon
  3

• Duplicated atom name

  #346 opened 2 years ago by kexul
  8

• Water name is not correctly converted in vacuum simulation

  #338 opened 3 years ago by xiki-tempula
  3

• Incorrect unit conversion?

  #332 opened 3 years ago by xiki-tempula
  1

• Inconsistent typing when doing unit conversions

  #329 opened 3 years ago by xiki-tempula
  2

• Support pow operator for all unit-based types

  #326 opened 3 years ago by xiki-tempula
  6

• Unit conversion

  #325 opened 3 years ago by xiki-tempula
  9