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I'm setting the last layer to Tanh, just for testing purposes instead of None like:
LinearLayer(width_layer,1,activation=nn.Tanh())
and get an error
```
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From KJE
You don’t mention anything about current state of art of modelling of micelles or coarse graining in micelle or other soft matter systems ie for totally computational systems, not those li…
arm61 updated
5 years ago
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Hi,
I tried coarse-graining the atomistic trajectory. But votca uses open boundary conditions instead of periodic boundary conditions.
I run the command:
```
csg_map --top topology.xml --trj A…
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**Is your feature request related to a problem? Please describe.**
For coarse-grained modeling, it is important to be able to manually specify which pairs of atoms are bonded together (instead of t…
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there is a FL (Frobenius Lagrange Decomposition) command but Perm2Coords is maybe not working anymore I think. I would like to be able to able to do what's in the cube paper, get coordinate form of…
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On a test dataset I compute neighbors and then immediately compute/plot both tSNE and UMAP and show them next to each other. Sometimes, we get pretty dramatic differences such as the one attached. I…
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Due to an internal reshuffling of the microstate sets, we observe misplaced and mislabeled network plots when using given positions and flux coarse graining; see markovmodel/pyemma#1004.
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Hi all,
it's not clear to me how to set the number of hidden states when calculating a hidden MSM. Should this number be equal to the number of microstates from prior clustering?
I am refering to py…
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I suggest a significant change in notebook 4 (may affect notebook 5 too).
First I would like to avoid the usage of the MSM method 'coarse_grain' because that currently just calls a HMM estimation.…