proteneer/timemachine

Issues

• Consider updating Forcefield serialization format

  #953 opened 4 months ago by maxentile
  1

• Possibly expand test coverage of set_params

  #1120 opened 4 months ago by maxentile
  1

• Check chiral consistency at the end-states

  #773 opened 4 months ago by proteneer
  1

• Modify cosine angle functional form

  #743 opened 8 months ago by proteneer
  12

• Distribute on conda-forge?

  #1261 opened 9 months ago by mikemhenry
  0

• Issue Building "contains a 128-bit integer, which is not supported in device code"

  #1257 opened 9 months ago by mikemhenry
  2

• Clean up GetMass calls

  #703 opened a year ago by jkausrelay
  0

• Which procedures require OpenEye?

  #1111 opened a year ago by ljmartin
  11

• Option to freeze `d_volume_scale` in barostat?

  #622 opened a year ago by maxentile
  3

• Consider unifying approach to PRNG state

  #980 opened 2 years ago by maxentile
  5

• Inconsistent conventions for axis ordering of `u_kln` matrices

  #1100 opened a year ago by mcwitt
  0

• Some lambda schedules fail validation when num_windows < 5

  #714 opened a year ago by maxentile
  0

• Fixing failing tests that are skipped due to speed

  #647 opened a year ago by badisa
  6

• Enable More C++ Warnings

  #617 opened a year ago by badisa
  0

• Consider upgrading to pymbar 4

  #830 opened a year ago by maxentile
  0

• Disconnected dummy atoms in some cases with complete_rings=False

  #1016 opened 2 years ago by mcwitt
  0

• Upgrade Python version

  #632 opened 2 years ago by mcwitt
  1

• Resolve ownership semantics of wrapped objects

  #791 opened 2 years ago by badisa
  3

• Constructing potential energy functions for many systems on same device

  #682 opened 2 years ago by maxentile
  6

• Improve (interpretation of) per-component diagnostics?

  #923 opened 2 years ago by maxentile
  0

• Consider adding force decomposition utility

  #886 opened 2 years ago by maxentile
  0

• Move processing of integrator parameters into C++

  #792 opened 2 years ago by badisa
  0

• Consider using `rich`

  #851 opened 2 years ago by maxentile
  0

• Add tests for numerical stability of intermediates in ring closing transformations

  #850 opened 2 years ago by mcwitt
  0

• Consider stabilizing `periodic_torsion` for nearly collinear inputs

  #848 opened 2 years ago by maxentile
  0

• Consider updating `DEFAULT_TEMP` from 300 K to 298.15 K

  #827 opened 2 years ago by maxentile
  0

• Possibly update charge symmetrization approach

  #817 opened 2 years ago by maxentile
  0

• Investigate Aligning Molecules with a minimizer

  #816 opened 2 years ago by badisa
  0

• Precommit hook to verify pybind stubs can require a complete new build

  #728 opened 2 years ago by badisa
  0

• update build instructions

  #779 opened 2 years ago by proteneer
  1

• Enable MCS to be more relaxed

  #774 opened 2 years ago by proteneer
  0

• deboggle: Combine common return arguments into a container

  #757 opened 2 years ago by jkausrelay
  0

• Revisit conformer generation for ELF10 charges

  #723 opened 3 years ago by jkausrelay
  0

• Modify some uses of jax numpy -> original numpy

  #717 opened 3 years ago by maxentile
  5

• Move miscellaneous files to attic

  #606 opened 3 years ago by maxentile
  0

• Spurious calls to execute_selective in Jax wrapper

  #706 opened 3 years ago by maxentile
  1

• Move reusable data and utilities into testsystems

  #710 opened 3 years ago by mcwitt
  0

• Consider moving timemachine module sources under `src/` directory

  #679 opened 3 years ago by mcwitt
  1

• custom_ops binary references local source paths

  #674 opened 3 years ago by mcwitt
  0

• Clean and DRY nonbonded potential code

  #639 opened 3 years ago by mcwitt
  0

• Consider merging `slow_tests/` back into `tests/` and using pytest markers?

  #611 opened 3 years ago by maxentile
  0

• Gradient estimator precision

  #667 opened 3 years ago by maxentile
  0

• Unexpected neighborlist behaviors when (n_atoms - 1) % 32 == 0

  #663 opened 3 years ago by maxentile
  2

• Switch to Gitlab CI

  #625 opened 3 years ago by badisa
  1

• Allow providing Seeds to RABFE Models

  #636 opened 3 years ago by badisa
  0

• Make reference, test argument ordering consistent in test assertions

  #635 opened 3 years ago by mcwitt
  0

• IndexError when molecule contains no improper torsions

  #623 opened 3 years ago by maxentile
  2

• Assertion error in enhanced.py::identify_rotatable_bonds

  #618 opened 3 years ago by maxentile
  0

• Refactor `proto/` module and move `parallel` to `timemachine/parallel/`

  #612 opened 3 years ago by badisa
  0

• Speed up slow tests in test_md.py

  #609 opened 3 years ago by maxentile
  3