choderalab yank-examples issues

choderalab / yank-examples

Examples for use of YANK - getyank.org

MIT License

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issues

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openmmtools.multistate.utils.SimulationNaNError: at abl-imatinib example

#91 iwatobipen closed 2 years ago
0
t4-lysozyme analyze error

#90 9527567 opened 2 years ago
3
Removed travis CI config file

#89 mikemhenry closed 3 years ago
0
Using yank for calculation of mixing free energy

#88 Eli-VDB opened 3 years ago
0
NAN encountered in freesolv example.

#87 kexul closed 4 years ago
7
[WIP] Add PHIPA examples

#86 jchodera opened 4 years ago
0
Update T4 Lysozyme examples

#85 andrrizzi closed 4 years ago
1
tip

#84 cescxiangyu closed 5 years ago
0
Test Yaml syntax only and update example files accordingly

#83 jaimergp closed 4 years ago
17
openmmtools.mcmc - Potential energy is NaN after 0 attempts of integration with move LangevinSplittingDynamicsMove Attempting a restart...

#82 agreen69 opened 6 years ago
4
Update examples for new `mcmc` and `samplers` YAML syntax

#81 jchodera opened 6 years ago
0
[WIP] Update all examples for SAMS

#80 jchodera closed 6 years ago
1
Comment error in host-guest example

#79 sgill2 opened 6 years ago
0
Link to phenol hydration tutorial is broken

#78 davidlmobley closed 6 years ago
2
Explicitly specify solvent_model in examples

#77 jchodera opened 7 years ago
0
Rename FreeSolv solutes from nonsensical "binders" to "solutes"

#76 jchodera opened 7 years ago
4
Fix typo in hydration free energy examples

#75 jchodera closed 7 years ago
1
Enable automated testing of examples; validate examples actually run

#74 davidlmobley opened 7 years ago
19
Hydration calculation uses extra lambdas in gas

#73 davidlmobley opened 7 years ago
7
minor editing of hydration example

#72 davidlmobley opened 7 years ago
2
Update the LSF scripts to use the `-q gpuqueue` flag

#71 Lnaden closed 7 years ago
0
Set resume_setup: yes in all of these examples

#70 jchodera opened 7 years ago
2
Update LSF Scripts for new SP GPU syntax

#69 Lnaden closed 7 years ago
2
Make examples setup normally as part-way travis fix.

#68 Lnaden opened 7 years ago
1
Fix typo

#67 jchodera closed 7 years ago
0
Update conda installation in travis to try to fix test failures

#66 jchodera closed 7 years ago
1
Mass update to the examples, works with YANK 0.17 and LSF

#65 Lnaden closed 7 years ago
1
Update YAML syntax for Abl:imatinib

#64 jchodera closed 7 years ago
1
Update README

#63 jchodera closed 7 years ago
0
Is everything broken?

#62 jchodera closed 7 years ago
0
binding/abl-imatinib example broken

#61 jchodera closed 7 years ago
6
Get Travis tests running again

#60 Lnaden opened 7 years ago
8
Yank ver 0.17 causes errors in the hydration phenol example

#59 nividic closed 7 years ago
4
How to input yank to run hydration free energy by using openmm serialized system (.xml) files

#58 nividic opened 7 years ago
13
Add slurm batch scripts

#57 jchodera opened 7 years ago
2
Typo in Abl-Imatinib yaml file?

#56 steven-albanese closed 6 years ago
1
Add some benchmark expectations for running the examples

#55 jchus opened 7 years ago
5
Prepped for Yank 1.0 Early Access release (0.14.1)

#54 Lnaden closed 7 years ago
3
Cut release

#53 jchodera closed 7 years ago
3
Turn on pack for binding examples and smiles ligands

#52 andrrizzi closed 7 years ago
5
CRITICAL: Pin to newer version of YANK once release has been cut and built

#51 Lnaden closed 7 years ago
2
Added back in water parameters since leaprc's got all shifted

#50 Lnaden closed 7 years ago
0
Phenol explicit water example error

#49 nividic closed 7 years ago
4
Examples don't give appropriate precision/sig figs

#48 davidlmobley closed 7 years ago
1
Question on implicit solvent example

#47 davidlmobley closed 7 years ago
2
Fix typo in implicit.yaml for phenol

#46 davidlmobley closed 7 years ago
1
Update conda recipe to latest yank version

#45 davidlmobley closed 7 years ago
6
Changed to use new location of ff14sb

#44 Lnaden closed 7 years ago
1
Add explicit solvent host-guest branch

#43 jchodera closed 7 years ago
3
Add explicit solvent option for host-guest example

#42 jchodera closed 7 years ago
1