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currently running two different ensembles, one with ADCIRC+BESTTRACK and one with NEMS+ADCIRC+BESTTRACK, both running from the same perturbation of track files (3 per variable over 4 variables: along-…
ghost updated
2 years ago
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Hi, I'm very interested in this work thanks for sharing.
I see that the code uses preprocessed h5ad files. I'd be interested to know how these data are produced from the source data e.g. [https://w…
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The batch size and which examples are in each batch can impact how a model learns during training. However, during evaluation, the batch size and which examples are in each batch should only impact t…
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I've had a quick shot at running ABFEs with SOMD2. The overall experience was a massive step up from SOMD! The recent sire documentation was also super clear and comprehensive. However, I've had a cou…
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Thank you for sharing this great dataset! It’s very useful for our work! In the process of using this dataset, I have a few questions:
1. Where can we find a detailed explanation of each category i…
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Hello,
When calculating the free energy change for a perturbation involving only dummy atoms to dummy atoms, MBAR gives exactly zero kcal/ mol, as expected, whereas TI gives positive free energies …
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when I run the script, I had the following error about nvcc
```
local/chain/tuning/run_tdnn_1j.sh
This script is intended to be used with GPUs but you have not compiled Kaldi with CUDA
If you w…
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Hi @dormrod ,
Thanks for this wonderful package! I plan to use it to generate equilateral triangle raft and I was wondering if it is possible to make all edges of equal length by tuning the potenti…
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According to [custom data turorial](https://github.com/snap-stanford/GEARS/blob/master/demo/data_tutorial.ipynb),
> (2) Create your own Perturb-Seq data
Prepare a scanpy adata object with
adat…
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* how does the function https://github.com/noaa-ocs-modeling/EnsemblePerturbation/blob/main/examples/adcirc/perturb_tides.py
work?
What's the strategy you guys use to perturb the tides to capture…