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BioSimSpace
Code and resources for the EPSRC BioSimSpace project.
https://biosimspace.org
GNU General Public License v3.0
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Issue in reproducing the funnel methadynamics tutorial
#428
velocirraptor23
closed
10 months ago
2
[BUG] Water molecule coordinates are setting to (0,0,0)
#427
ale94mleon
closed
1 year ago
4
Reporting a vulnerability
#426
igibek
opened
1 year ago
0
[BUG]
#425
jasmin-guven
closed
1 year ago
10
Feat alchemlyb2
#424
xiki-tempula
closed
1 year ago
3
Adition of parameters for cofactors like NADPH or FADH
#423
velocirraptor23
closed
1 year ago
2
AnalysisError: SOMD free-energy analysis failed!
#422
velocirraptor23
closed
1 year ago
5
[BUG] Cannot import BioSimSpace after installation of biosimspace 2023.1.2 using mamba
#421
cespos
closed
1 year ago
3
Sync with openbiosim/devel
#420
lohedges
closed
6 months ago
2
[BUG] OSError "It looks like you failed to include a topology file." when reading SDF which doesn't contain redundant bond order information
#419
noahharrison64
closed
1 year ago
10
Are atomtypes meant to be updated when using repartitionHydrogenMass?
#418
noahharrison64
opened
1 year ago
16
Sync with OpenBioSim/devel [closes #416]
#417
lohedges
closed
1 year ago
16
Sync the two branches
#416
xiki-tempula
closed
1 year ago
1
Pickling a parametrised molecule from an SDF file with GAFF2
#415
msuruzhon
closed
1 year ago
4
Absolute Binding Free Energy Calculations with GROMACS
#414
fjclark
closed
1 year ago
7
`_toRegularMolecule` failing with `convert_amber_dummies=True`
#413
msuruzhon
closed
1 year ago
15
BioSimSpace.Align.viewMapping: py3Dmol.view not rendering in Jupyter Notebook
#412
lohedges
closed
1 year ago
11
Changed `_k_boltz` to `_k_boltz.value()` to get the underlying value …
#411
chryswoods
closed
1 year ago
2
Unable to import BioSimSpace after mamba installation
#410
akalpokas
closed
1 year ago
12
Would it be possible to include HiMap as an alternative to LoMap in the generateNetwork method?
#409
DreamCykl
closed
1 year ago
2
Updates following Sire 2023 API changes
#408
lohedges
closed
1 year ago
24
Make _removeDummies() recognise dummy bonds
#407
msuruzhon
closed
1 year ago
10
Fix dummy atom handling during hydrogen mass repartitioning
#406
lohedges
closed
1 year ago
1
Making HMR work with dummies
#405
msuruzhon
closed
1 year ago
11
Problem when converting Gro/Top to Rst7
#404
msuruzhon
opened
1 year ago
12
CVE-2007-4559 Patch
#403
TrellixVulnTeam
closed
6 months ago
0
Add support for autodection of disulphide bonds during parameterisation
#402
lohedges
closed
1 year ago
9
Use report_interval for the frequency of storing the energy for Gromacs process.
#401
xiki-tempula
closed
1 year ago
0
Is it possible to add ions to an already solvated system, without adding any more water molecules?
#400
aniketsh
opened
1 year ago
4
Add position restraint to all protocols
#399
xiki-tempula
closed
1 year ago
0
Fix CI issues following EXS sandpit merge
#398
lohedges
closed
1 year ago
12
Make sure ordering is preserved when a molecule is replaced
#397
lohedges
closed
1 year ago
10
HILLS file not updating during restarting simulation
#396
rubinanoor9
closed
1 year ago
4
Storage quota exceeded on the Anaconda cloud
#395
lohedges
closed
1 year ago
1
Fix offset when injecting position restraints into GROMACS top file
#394
lohedges
closed
1 year ago
3
Strategy for migration to OpenBioSim GitHub organisation
#393
lohedges
closed
1 year ago
1
Correction for funnel metadynamics
#392
guidsari
closed
1 year ago
3
Inconsistent Reporting of Dihedral Energies
#391
fjclark
closed
1 year ago
5
UnboundLocalError when loading Chamber topology file.
#390
TENeary
closed
1 year ago
2
Paramaterising with openff issues
#389
annamherz
closed
1 year ago
13
Merging devel into main for the 2023.0.0 pre-release
#388
lohedges
closed
1 year ago
0
BioSimSpace.IO.readMolecules failed to read amber prm7 and rst7 file
#387
Naf-Guo
closed
2 years ago
2
'BioSimSpace._SireWrappers.System' can only contain unique molecules.
#386
kexul
closed
2 years ago
8
CI hangs / timeouts
#385
lohedges
closed
2 years ago
1
OpenFF and AmberTools
#384
lohedges
closed
1 year ago
14
The correct way of setting up the env for BSS for CI
#383
xiki-tempula
closed
2 years ago
25
Use the Free Energy Analysis pipeline from alchemlyb
#382
xiki-tempula
closed
2 years ago
2
Ensure absolute works with new analysis options
#381
fjclark
closed
2 years ago
0
Allow Native SOMD Analysis to Use Compressed Input
#380
fjclark
closed
2 years ago
0
Allow Native SOMD analysis to use .bz2 files
#379
fjclark
closed
2 years ago
0
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