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[WIP] SepTop Protocol#1057

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hannahbaumann wants to merge 92 commits intoOpenFreeEnergy:mainOpenFreeEnergy/openfe:mainfrom hannahbaumann:start_septophannahbaumann/openfe_septop:start_septopCopy head branch name to clipboard

+13,628

Commits

Commits on Oct 23, 2024

• Initial commit SepTop settings

  hannahbaumann

  committed
  3a64347

Commits on Oct 24, 2024

• Initial SepTop protocol work

  hannahbaumann

  committed
  066c47b

• Some fixes

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  committed
  08ef427

• Implement a Setup unit and empty Run unit

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  committed
  26b4b92

Commits on Oct 25, 2024

• Updating positions in the solvent and complex

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  committed
  3261ba2

Commits on Nov 11, 2024

• Add some femto utils, setup alchemical system

  hannahbaumann

  committed
  b9c4e70

Commits on Nov 15, 2024

• Work on implementing restraints

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  committed
  43fc5af

Commits on Nov 19, 2024

• Some more changes

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  committed
  d8ff3b1

• Add some femto utils

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  committed
  5753689

• Some fixes for the restraints

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  3a71963

• Create separate solvation settings for solvent and complex

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  0b6d7ba

• Testing some things

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  6894cd9

• Testing some things

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  107d603

• Fix comp_resids_B

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  2a017d5

• Fix restraints complex mdtraj

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  74a9818

• Update restraint selection

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  427aee4

Commits on Nov 20, 2024

• More edits Boresch restraints

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  8b88214

• Change type check restraints

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  52992d8

• Changes unitcell lengths

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  5a90c55

• Small test unit cell

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  b4ffd2b

Commits on Nov 21, 2024

• Update unit cell length

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  0e32007

• Update unit cell length2

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  90b1679

• small fix

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  3ca733d

• More changes restraints

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  82da7c8

• Print statements to help troubleshoot restraints

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  df637bc

• Update indices

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  c4671e4

• Fix units

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  ae1a2b4

• Update units

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  5ca9923

• Small fixes

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  committed
  ca72561

Commits on Nov 22, 2024

• Change lambda settings

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  fe1bad6

Commits on Nov 26, 2024

• Serialize system

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  e4713a4

• small fix

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  9eb40d2

• Only store system, topology

  hannahbaumann

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  6f53741

• Start of run unit

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  0a5206c

• Add run unit to create method

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  5d0c10f

• Add missing import

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  8cafbe8

Commits on Nov 27, 2024

• Write run unit

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  committed
  2829604

• Remove unnecessary import

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  52eef2e

• Remove verbose

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  eda32c2

• Add states to run unit

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  7663e2d

• Add simtype

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  1551bc2

• Remove nocutoff

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  eebff50

• Small fixes

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  committed
  4a5922d

• Change monotonic check

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  bcaefd8

• Put troubleshooting pdb files in the sharedbase path for now

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  23aecb5

Commits on Nov 28, 2024

• Fix scaling restraints

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  27e1ea7

• Update boresch scaling

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  026a0ef

• testing something

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  a78481f

Commits on Dec 2, 2024

• Test out not doing a preequ

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  b262a9e

• Change min length solvent

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  063c59a

Commits on Dec 3, 2024

• Change phase detection

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  702b639

• Adding print statements for debugging

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  13c7724

Commits on Dec 4, 2024

• Add print statements to help debug

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  6b393d5

• Save prequ file

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  f86601e

• Run short equ

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  committed
  7372985

• Update gather to separate setup and run results

  hannahbaumann

  committed
  a401c98

Commits on Dec 5, 2024

• Fix gather

  hannahbaumann

  committed
  c2e2d8a

Commits on Dec 6, 2024

• Testing out using the openmmtools alchemical factory instead of femto

  hannahbaumann

  committed
  588a1d2

• Add imports

  hannahbaumann

  committed
  b7f7a50

Commits on Dec 9, 2024

• Adapt Lambda states

  hannahbaumann

  committed
  4159e69

• Add individual lambda restraints

  hannahbaumann

  committed
  1ce8dba

• Small FIx

  hannahbaumann

  committed
  97f0285

• Fix restraints sign

  hannahbaumann

  committed
  51ebfac

Commits on Dec 10, 2024

• More tests and fixes

  hannahbaumann

  committed
  bd69a8b

• More updates

  hannahbaumann

  committed
  b4c06ba

Commits on Dec 11, 2024

• Merge branch 'main' into start_septop

  hannahbaumann

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  274c204

• Update compute location

  hannahbaumann

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  e6dae2f

• Small fix

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  committed
  782de90

• Adding some more docstrings

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  14ae69f

Commits on Dec 12, 2024

• AlchemicalFactory changes

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  e4c25e1

Commits on Dec 13, 2024

• Add slow energy test

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  e780a94

• Move energy test to slow

  hannahbaumann

  committed
  b5cdaf4

• Fix energy test

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  ee984b4

• Fix off molecule

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  committed
  8796be2

Commits on Dec 16, 2024

• Merge branch 'main' into start_septop

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  43ad90b

• Subclass Parameterstate

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  6c628dd

• Change AlchemicalRegion name

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  92690d8

• Update restraint lambda parameter

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  2d1eba4

• Update settings

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  committed
  3849778

• Change alchemical state def

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  d989feb

Commits on Dec 17, 2024

• Remove copy of AlchemicalFactory

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  6311a92

• Remove femto alchemy

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  committed
  bc489e3

• Remove unnecessary file

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  committed
  228c1c9

• Small fixes

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  committed
  a727ec2

• Some fixes

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  committed
  32e541f

• Update tests

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  committed
  a7d7b2e

Commits on Dec 18, 2024

• Merge branch 'main' into start_septop

  hannahbaumann

  authored
  2d42497

Commits on Dec 19, 2024

• Add tests protocol results

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  committed
  ac9f1a8

• Merge branch 'main' into start_septop

  hannahbaumann

  authored
  22f9b79

Commits on Dec 20, 2024

• debug failing test

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  committed
  d1d1b04

• Test restraints closer

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  153ffec

• Test restraints closer 2

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  9efab61