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for k in 28 27 25 23 21 19 17 15 13 11 9 7 5 3 1; do python -u mnist_classification_wholenetwork.py ./data --target_size $k --num_hidden_features $j --num_train_samples 60000 --fileprefix relulr0.1…
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Hi, is there a method in Deeptime similar to Pyemma's " pyemma.coordinates.save_traj" which can be used to extract pdb structures representing macrostates after coarse-graining using PCCA+
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**Is your feature request related to a problem? Please describe.**
[Huybers (2022)](https://doi.org/10.1175/JCLI-D-22-0011.1), analyzing the spectral content of a portion of the GISP2 d18O record, m…
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I want to use the FlowSieve package to compute the kinetic energy spectrum. It uses a coarse-graining approach, which does not have the limitations of the Fourier transform and handles boundaries well…
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We are working on Chignolin Coarse Grain Tutorial from this repository:
https://github.com/torchmd/torchmd-cg.git
We are working on a Machine Learning project pertaining to Coarse-graining of prot…
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I saw the article "Protocols for Multi-Scale Molecular Dynamics Simulations in Amber and Gromacs: a Case Study of Intrinsically Disordered Amyloid Beta" from biorxiv. I want to use your method to repr…
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I am unable to get coarse grain files when I enter the smiles for silica or alpha cristobalite. Is auto_martini not able to make silica CG structure?
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Pyan3 could use some postprocessing support:
- In a mid-sized or large project, it's currently easy to lose sight of the forest for all the trees (pun not intended). The visualization of all indivi…
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in the spirit of Aluie et al 2017, JPO, doi:10.1175/JPO-D-17-0100.1
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TODO comments from `mbuild/coarse_graining.py`
```
179-def _create_proxy_labels(real_thing, memo):
180- if not is_leaf(real_thing):
181- for label, part in real_thing.labels.items():
18…