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Protocol to run plain MD simulations #516

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Dec 28, 2023
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1610300
start plain MD scripts
hannahbaumann Jul 31, 2023
e64fb75
Add tests, fixing some errors in methods
hannahbaumann Aug 1, 2023
86a60c9
Add gathertest
hannahbaumann Aug 2, 2023
b9c8413
Add StateDataReporter
hannahbaumann Aug 2, 2023
f33e21d
Cleanup functions
hannahbaumann Aug 3, 2023
72ee364
fix integrator units
hannahbaumann Aug 3, 2023
1516300
fix setvelocity unit
hannahbaumann Aug 3, 2023
b9f9b6d
test reporter
hannahbaumann Aug 3, 2023
033a9ac
change reporter to xtc
hannahbaumann Aug 3, 2023
3901dfa
change reporter to dcd
hannahbaumann Aug 3, 2023
dbcacf3
clean up reporters
hannahbaumann Aug 4, 2023
7b4c04d
Add checkpoint reporter
hannahbaumann Aug 7, 2023
95b9c16
change reporter to xtc
hannahbaumann Aug 7, 2023
96b69f0
Fix reporters
hannahbaumann Aug 7, 2023
fca9c23
Fix StateReporter
hannahbaumann Aug 7, 2023
48b626c
Add output indices traj and other fixes
hannahbaumann Aug 7, 2023
ed79587
merge changes
hannahbaumann Aug 7, 2023
ac15045
Merge branch 'main' into plain_md
hannahbaumann Aug 8, 2023
0b61cbf
changes test
hannahbaumann Aug 8, 2023
559d18d
Merge branch 'main' into plain_md
hannahbaumann Aug 15, 2023
e77cad6
style_fix
hannahbaumann Nov 3, 2023
3b0f212
Merge branch 'plain_md' of https://github.com/OpenFreeEnergy/openfe i…
hannahbaumann Nov 3, 2023
e0ea862
remove preequil
hannahbaumann Nov 6, 2023
4b52c25
Change system name
hannahbaumann Nov 8, 2023
8338cf3
Save pdb of the system and of minimized structure
hannahbaumann Nov 9, 2023
9c74b84
Fixes plain MD method
hannahbaumann Nov 14, 2023
3ff34e2
Fix docstring
hannahbaumann Nov 17, 2023
22eec31
Add ffcache test
hannahbaumann Nov 17, 2023
e160600
Add NVT and NPT equilibration
hannahbaumann Nov 20, 2023
24d5a2f
Fix equilbration settings
hannahbaumann Nov 20, 2023
0c66327
Change get_simsteps to handle NVT equilibration
hannahbaumann Nov 20, 2023
df7f921
Fix positions for pdb storage
hannahbaumann Nov 20, 2023
a51def2
Fix get_simsteps tests
hannahbaumann Nov 21, 2023
c5f5667
Disable barostat for NVT equilibration, bring it back for NPT
hannahbaumann Nov 21, 2023
2f586a9
Output pdb file after NVT equilibration and after NPT equilibration
hannahbaumann Nov 21, 2023
9170413
Add without_oechem_backend wrapper
hannahbaumann Nov 21, 2023
b33bc7a
Add log_system_probe
hannahbaumann Nov 21, 2023
8049534
Add verbosity flag
hannahbaumann Nov 21, 2023
97171dc
Small fixes
hannahbaumann Nov 21, 2023
b3bb0eb
Pep8 fixes
hannahbaumann Nov 21, 2023
d0fbe97
Change system naming
hannahbaumann Nov 21, 2023
4fbf74f
Move actual MD stuff into separate function to be used in other proto…
hannahbaumann Nov 22, 2023
323f1e8
Small fixes
hannahbaumann Nov 22, 2023
40978e4
Add benzene_modifications
hannahbaumann Nov 22, 2023
e5c470b
Merge branch 'main' into plain_md
hannahbaumann Nov 22, 2023
1507305
Remove benzene_modifications
hannahbaumann Nov 22, 2023
be8c4f2
Merge branch 'plain_md' of https://github.com/OpenFreeEnergy/openfe i…
hannahbaumann Nov 22, 2023
8cffa42
Change to smc_components
hannahbaumann Nov 22, 2023
c119917
Move repeat_settings to protocol
hannahbaumann Nov 22, 2023
11ff8ca
Change from equ_x to equil_x
hannahbaumann Nov 22, 2023
9473a96
Change comp_type
hannahbaumann Nov 22, 2023
b63ae2a
Remove stateB from ProtocolUnit
hannahbaumann Nov 22, 2023
db4a847
Use individual settings for _run_MD function
hannahbaumann Nov 22, 2023
0d527e0
Small fix
hannahbaumann Nov 22, 2023
7ed3f5d
Merge branch 'main' into plain_md
hannahbaumann Nov 22, 2023
98aa2ba
Fix npt issue
hannahbaumann Nov 22, 2023
8d186ac
Merge branch 'plain_md' of https://github.com/OpenFreeEnergy/openfe i…
hannahbaumann Nov 22, 2023
8aa64a6
small fix
hannahbaumann Nov 22, 2023
5b9b572
small fix2
hannahbaumann Nov 22, 2023
ed0c5b5
Merge branch 'main' into plain_md
hannahbaumann Nov 23, 2023
3996e37
Add test for result json file
hannahbaumann Nov 23, 2023
eca1b01
Merge branch 'plain_md' of https://github.com/OpenFreeEnergy/openfe i…
hannahbaumann Nov 23, 2023
27b9b42
Add results json files for MD run
hannahbaumann Nov 23, 2023
2d6e38e
Add tests for logging output
hannahbaumann Nov 23, 2023
45890d4
Add init files
IAlibay Nov 22, 2023
552e31b
Merge branch 'main' into plain_md
IAlibay Nov 23, 2023
f5e6d99
Changes __init__.py
hannahbaumann Nov 24, 2023
146b8d5
add return annotation for results
hannahbaumann Dec 7, 2023
71f09d1
Update openfe/protocols/openmm_md/plain_md_methods.py
hannahbaumann Dec 7, 2023
085919d
make settings names more specific
hannahbaumann Dec 7, 2023
f21a7b1
change results.json file with new settings names
hannahbaumann Dec 8, 2023
7f46b7f
change run method to take temp and barostat_frequency instead of full…
hannahbaumann Dec 8, 2023
f8ec471
add slow test
hannahbaumann Dec 8, 2023
39803e5
fix test
hannahbaumann Dec 8, 2023
b9c924b
Update openfe/protocols/openmm_md/plain_md_methods.py
hannahbaumann Dec 12, 2023
4704336
Change purepath to path
hannahbaumann Dec 12, 2023
64109d8
Change PurePath to Path
hannahbaumann Dec 13, 2023
b16d91d
Merge branch 'main' into plain_md
IAlibay Dec 28, 2023
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20 changes: 20 additions & 0 deletions openfe/protocols/openmm_md/__init__.py
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Original file line number Diff line number Diff line change
@@ -0,0 +1,20 @@
# This code is part of OpenFE and is licensed under the MIT license.
# For details, see https://github.com/OpenFreeEnergy/openfe
"""
Run MD simulation using OpenMM and OpenMMTools.

"""

from .plain_md_methods import (
PlainMDProtocol,
PlainMDProtocolSettings,
PlainMDProtocolResult,
PlainMDProtocolUnit,
)

__all__ = [
"PlainMDProtocol",
"PlainMDProtocolSettings",
"PlainMDProtocolResult",
"PlainMDProtocolUnit",
]
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