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The purpose of this issue is to suggest building a "component" for auto_martini (dubbed `mmic_ffpa_autom`) that makes it part of the [MMIC](https://mm-portal.netlify.app/mmic) ecosystem [MolSSI](http:…
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I seem to be making good progress with the `minRMSD` based equitemporal clustering. You can see my results for the matrix of Src/Abl single/ensembler projects (cc: #23) here on the cluster:
```
/cbio…
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Dear @giorgionicoletti,
I recently encountered your research and publication on PRG, and I appreciate the insights you provided. I am currently working through your PRR 2020 paper and attempting to…
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**Describe the bug**
Generating a residue graph for proteins, connected by an EN with non-unique resids fails. This leads to some scrambling in the coordinate reading. This only affects highly symmet…
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Hello, everyone!
I am confused about the searching range of the coarse-grain operation. Supposing filter scale = 100km and Kernel_opt = 4 which is a tanh kernel. I noticed that there is a Kernpa…
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The order (indices) of the coarse grained states obtained by
fluxAB = msm.tpt(M, A, B)
fluxAB.coarse_grain(my_coarse_sets)
is unclear. A is always at index 0 and and B is always at index n, bu…
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I want to understand the how the thermodynamics and kinetics has changed due to ligand binding. So we have performed several short (1 microsecond) MD simulation with and without ligand.
We are using…
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Thanks for the cool library!
I find there are binary values for Transfer Entropy input. such as :
`xs = [0,1,1,1,1,0,0,0,0]
ys = [0,0,1,1,1,1,0,0,0]`
Is it possible to use continuous values i…
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Provide self-updates on the progression of the project through a stand-up or daily scrum type format.
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This thread is intended to collect some concrete use cases for adding first-class support for quantum machine learning (QML) use cases.
We have identified several classes of use cases we would lik…