[WIP] Free energy fitting - #54

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free-energy-fitting

Commits on Oct 22, 2020

Create run on openff-1.2 training dataset.ipynb
maxentile
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79d125f
use offmol_indices, handle case of no propers / impropers, and adhere to 79 character lines
maxentile
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e3454ac
allow to .sum(dim=1) even when there are no impropers
maxentile
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d3f236d

Commits on Oct 24, 2020

allow impropers to have length 0 in valencemodel
maxentile
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10268d5

Commits on Oct 25, 2020

add gbsa port
maxentile
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9c350ee
oof, avoid pytorch in-place modification of input argument tensors
maxentile
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cf14a20
gahh, careless variable-name typo
maxentile
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0c20732
wip demo notebook for fitting to a hydration free energy calculation with a graph-net in the loop
maxentile
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32f7d2d
port @proteneer's GBSA implementation instead
maxentile
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dfce74c
repeat fitting-to-free-energies notebook with less-likely-to-be-buggy PyTorch GBSA
maxentile
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6a02086

Commits on Oct 29, 2020

Commits on Oct 30, 2020

add missing conversion from nm/(proton_charge**2) to kJ/mol

maxentile
and
jchodera
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b564fe6
update gbsa docstring
maxentile
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08a2bcf
update freesolv-fitting notebook
maxentile
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d5ae749
re-run demo notebook with increased stepsize and decreased network size: validation set RMSE 1.8kcal.mol
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bacb705
ipynb --> py
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6d4c831
refine fit_freesolv.py script
maxentile
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9ffa304
add pdf figures from fit_freesolv
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7115efb

Commits on Oct 31, 2020

notebook reporting on element coverage in freesolv
maxentile
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c63bc05
oops, forgot nitrogen!
maxentile
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6db4016
notebook fitting to {C, H, O} mini-freesolv
maxentile
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9857f52
oodles o' vacuum samples
maxentile
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8e50eec
set openmm_cpu_threads to 1
maxentile
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1f1f520
Create fit to {C, H, O, N, Cl} subset of freesolv (n=529).ipynb
maxentile
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38bbf03
oops fix plot labels
maxentile
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7de7b6c
merge freesolv vacuum sample records
maxentile
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2643694
git lfs track freesolv_vacuum_samples.npz (279MB)
maxentile
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d24b5bf
add xyz column to freesolv_with_samples.h5
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e6d31d9
update {C, H, O} subset experiment to use thorough equilibrium sampling
maxentile
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98f424f

Commits on Sep 3, 2021

Add todos
maxentile
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0a06d43
Add SAGEConv
maxentile
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3c7eee4
Address GraphSAGE todo
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fad31a5
Update PDF figures
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ccea6ba