AlkEthOH (rings) snapshots and energies #23

maxentile · 2020-06-03T20:44:47Z

Continuing from #20 , adding configuration snapshots, MM energies, and "ab-initio-like" energies

Done:

Generate dataset of ~1million configuration snapshots (1000 per molecule, for the ~1000 molecules of AlkEthOH rings set, by 500K MD), with accompanying Parsley and ANI-1ccx potential energies, as well as parameterized system objects. (Tracked with Git LFS.)

Todo:

Provide efficient PyTorch DataLoader views of this dataset (incorporating choices made in AlkEthOH interaction-typing task #20 and started here some dataset structure #22 )
Complete and streamline non-graph-net neural baseline for energy regression on this set, "with an MM model as a layer"

Followup:

Expand to other molecule sets as planned

now being tracked by git-lfs

note that OpenEye Omega conformer generation failed for 906 of 1156 of these (results are produced for 250 of 1156) this is due to an issue that was addressed in openforcefield/openff-toolkit#517 -- will need to update to use latest development version of openforcefield toolkit instead of 0.6.0 ...

should revert this when 0.7.0 is released

Each of the 1156 molecules in the AlkEthOH rings set was parameterized using OpenFF 1.0.0 Parsley. Serialized OpenMM systems are saved for each parameterized molecule are saved. Each molecule is simulated in vacuum at 500K for 1 nanosecond, using the script in mm.py. (Simulation details: BAOAB Langevin thermostat, 1fs timestep, collision rate of 1ps, configuration snapshot saved every 1ps). Snapshots are saved using mdtraj, which stores xyz coordinates in units of nanometer. Molecular mechanics energies and ANI-1ccx energies for each of these ~1million snapshots are also saved in units of kJ/mol.

hmm, minimization problem for bond and angle terms, torsions are solved though...

…onversion with call to torchani.units

…1ccx forces also

…scripts/independent_params

also, adjust so that it's randomly initialized between 0 and 2 * true value

…and langevin

…into alkethoh-mm

lgtm-com · 2020-08-24T16:52:24Z

This pull request introduces 20 alerts when merging ccab4cf into cb0805c - view on LGTM.com

new alerts:

10 for Unused import
4 for Unused local variable
3 for Non-callable called
2 for Variable defined multiple times
1 for Module is imported with 'import' and 'import from'

maxentile and others added 30 commits May 27, 2020 18:06

ignore pycharm, .DS_Store

5f6f55d

alkethoh rings interaction-typing dataset

9dc8cd4

fix key error: 'Torsions' --> 'ProperTorsions'

bdeccba

save also openff mols

c91dce0

dicts instead of lists for mols and labeled_mols

6953869

initial rule-based baseline typers

78cd003

spruce up molecule-labeling script

5a04528

add type hints and reduce duplicated code alkethoh/baseline_typers

8859561

add alkethoh dataset using lfs

305f56a

Create pytorch_datasets.py

3c96239

string indices --> integer indices

f836827

remove AlkEthOH dataset files from .gitignore

cf91010

now being tracked by git-lfs

hgfp/data --> espaloma/data

8e0a3d3

local paths --> pkg_resources.resource_filename's

973d5e1

pin openff dependency at 0.6.0+443.g97d31e6f

7dcac83

should revert this when 0.7.0 is released

dataset

a6eb837

save also serialized openmm system

3f1ca71

fix mindless unit typo

7313e10

add script to compute ANI-1ccx energies on all snapshots

4f8755b

fix mindless file suffix typo

b7dcc0e

start to write dataset

d1ca069

typing data

1f83880

bug fix

bccf76f

not print

8da1a57

skip net test

7b39135

collate_fn

2fa0b4e

save and load test

2e19483

collection

152ff11

maxentile added 29 commits August 21, 2020 16:21

define loss function

d27b343

get forces by group

acf0908

harmonic-bond target

6f48918

angle and torsion targets

23bd5d5

initializing from reasonable bond-length

ad33064

hmm, minimization problem for bond and angle terms, torsions are solved though...

initialize from MM parameters

6aeba0b

initialize also from MM angle parameters

3279b45

switch to ani-1ccx target, try also basinhopping optimizer

628bc96

docstrings

ad315ac

add alternate parameterization for harmonic potentials

9bd87a6

refactor get_{bond|angle|torsion|nb}_energy util functions

dfe6fe0

save ANI-1ccx forces for all snapshots, replace hartree-to-kcal/mol c…

d97e9e9

…onversion with call to torchani.units

update snapshots_and_energies_with_ani1ccx to include computed ANI-…

0b660e9

…1ccx forces also

draft factor net

6bad41a

add (factor, contains, atom) edges

b314dc4

FactorToAtom messages

cbdbead

repeat

4717c44

module

2befd7e

path --> resource_filename(path)

2119f9a

apply to torsion perception task

1911511

apply to angle perception task

15d0a53

structures for initializing torsions at openff parameters

a5d4fa1

noticed a typo in mm.functional.linear_mixture

ff1e648

refeactor independent_params baseline script from /data/alkethoh to /…

d67199e

…scripts/independent_params

add fit_angles_to_forces.py

59ca320

also, adjust so that it's randomly initialized between 0 and 2 * true value

add fit_torsions_to_forces.py

7c2721a

factor out initialize_{bonds|angles|torsions}

b417213

factor out initialize_{bonds|angles|torsions}, add linearized params …

c08855e

…and langevin

Merge branch 'alkethoh-mm' of https://github.com/choderalab/espaloma …

ccab4cf

…into alkethoh-mm

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AlkEthOH (rings) snapshots and energies #23

AlkEthOH (rings) snapshots and energies #23

maxentile commented Jun 3, 2020

lgtm-com bot commented Aug 24, 2020

AlkEthOH (rings) snapshots and energies #23

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AlkEthOH (rings) snapshots and energies #23

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maxentile commented Jun 3, 2020

lgtm-com bot commented Aug 24, 2020