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choderalab
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espaloma
Extensible Surrogate Potential of Ab initio Learned and Optimized by Message-passing Algorithm 🍹https://arxiv.org/abs/2010.01196
https://docs.espaloma.org/en/latest/
MIT License
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Use rtd for docs
#167
mikemhenry
closed
11 months ago
7
Fix loading molecules serialized with older openff-toolkit versions (<=0.11)
#166
ijpulidos
closed
11 months ago
2
Switch to using Read the Docs
#165
mikemhenry
closed
11 months ago
3
Improved deployment testing with different charge-method options
#164
ijpulidos
closed
11 months ago
1
add comment to why some input features were commented out
#163
kntkb
closed
11 months ago
1
Add comment to why the input features were changed
#162
kntkb
closed
11 months ago
0
update default openff when creating system from graph (fix #160)
#161
kntkb
closed
11 months ago
1
Change default forcefield to latest openff
#160
ijpulidos
closed
11 months ago
2
Fail to train on gen2 dataset
#159
Guackkk
opened
1 year ago
1
example "Deploy espaloma 0.2.0" breaks
#158
micaela-matta
closed
11 months ago
8
Support different improper torsion multiplicity
#157
kntkb
closed
1 year ago
1
Cannot change improper torsion multiplicity
#156
kntkb
closed
1 year ago
0
Support newer versions of OpenFF Toolkit
#155
mattwthompson
closed
1 year ago
1
[DNM] Test if dgl 0.8.2 will work
#154
mikemhenry
closed
1 year ago
2
Support for modern openff-toolkit versions (>=0.11)
#153
ijpulidos
closed
1 year ago
1
Fix CI -- updated
#152
ijpulidos
closed
1 year ago
3
Fix data split
#151
kntkb
opened
1 year ago
1
Docstring for sequential.py is outdated
#150
kntkb
closed
1 year ago
0
Dataset splitting does not work as intended for some cases
#149
kntkb
opened
1 year ago
0
input invariance to resonance
#148
yuanqing-wang
closed
1 year ago
0
Environment yaml file with explicit versions
#147
simonaxelrod
closed
11 months ago
3
Add docs on downloading new QCFractal datasets (or including your own) and building new force fields
#146
jchodera
opened
1 year ago
1
Saving prmtop files from espaloma parameterization
#145
mmagithub
opened
1 year ago
4
Node featurization does not properly assign hybridization using OpenEye toolkit
#143
kntkb
closed
1 year ago
2
Changed default charge method to nn.
#142
madilynpaul
closed
11 months ago
13
Charge Method Question
#141
madilynpaul
closed
11 months ago
4
fix nonbonded force subtraction from reference derivative
#140
kntkb
closed
1 year ago
0
Nonbonded forces not properly subtracted from reference derivative
#139
kntkb
closed
1 year ago
0
[Question] Evaluating Amber ff14SB and espaloma on Pepconf
#138
LeifSeute
opened
1 year ago
0
Add CodeQL workflow for GitHub code scanning
#137
lgtm-com[bot]
closed
11 months ago
0
[Question] Datasets for reproduction of the QM results in the paper
#136
LeifSeute
closed
1 year ago
1
Question: example code for setting up MD simulation of protein-ligand complexes
#135
mganahl
closed
1 year ago
1
[Bug Fix] Cannot properly update forces when nonbonded interactions are subtracted from graph nodes
#134
kntkb
closed
1 year ago
2
get rid of large storage
#133
yuanqing-wang
closed
1 year ago
0
fix yaml syntax issue
#132
mikemhenry
closed
1 year ago
2
Add quick start to README
#131
mikemhenry
closed
11 months ago
1
AttributeError: 'float' object has no attribute 'value_in_unit' (and others)
#130
mikemhenry
opened
1 year ago
9
Pin to older toolkit + fix CI
#129
mikemhenry
closed
1 year ago
5
Update install instructions
#128
mikemhenry
closed
11 months ago
0
Rename master branch to main
#127
mikemhenry
closed
11 months ago
1
Cannot subtract nonbonded interactions
#126
kntkb
closed
1 year ago
0
[Question] Retraining espaloma model to include nonbonded potentials
#125
nbruciaferri
closed
1 year ago
1
Subtract nonbonded
#124
kntkb
closed
1 year ago
5
[Question] Getting Free Energy results and plots
#123
dinsausti
opened
1 year ago
1
Formal charge fix
#122
jthorton
closed
1 year ago
2
Total charge incorrect
#121
jthorton
closed
1 year ago
1
Cannot download zinc dataset for atom typing model reproducing
#120
qcxia20
opened
2 years ago
2
Add documentation link to README.md
#119
kntkb
closed
2 years ago
1
scripts to prepare denali dataset for training
#118
jeherr
opened
2 years ago
7
Fix readme link to docs
#117
mikemhenry
closed
1 year ago
1
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