release 0.9.0

New release 0.9.0 (after almost 2 years...)

• new features (dihedral ensemble analysis workflow)
• dropping support for old Python versions (sorry, too difficult to maintain and keep up with the Python eco system)
• GROMACS 4.6.5 to 2024.3 tested
• bug fixes and various quality-of-life improvements (e.g. black formatting, automated deployment, ...)

See CHANGES for the concise summary and below for list of merged PRs.

What's Changed

• changed dihedral atom group selection strings in test_dihedral.py by @cadeduckworth in #218
• CI updates by @orbeckst in #220
• Update em_charmm.mdp by @VOD555 in #210
• use new micro mamba action by @orbeckst in #221
• developing back end run methods by @cadeduckworth in #216
• Support toluene solvent by @VOD555 in #224
• Support cgenff toluene by @VOD555 in #228
• Fix setup and support toluene in mdpow-solvationenergy by @VOD555 in #230
• Use AutoMBAR instead of MBAR by @VOD555 in #234
• Automated Dihedral Analysis by @cadeduckworth in #217
• Periodic Angle Padding by @cadeduckworth in #242
• Workflows Base Module by @cadeduckworth in #229
• update banner logging by @orbeckst in #247
• Update statistical inefficiency calculation with statistical_inefficiency in alchemlyb 2.1.0 by @VOD555 in #250
• drop python 3.7 and testing improvements by @orbeckst in #249
• test on GROMACS 2022 and 2023 by @orbeckst in #255
• use relative imports inside MDPOW by @orbeckst in #257
• update to mamba-org/setup-micromamba by @orbeckst in #258
• Dihedral Plots: RDKit Mol Object by @cadeduckworth in #243
• Review all kwargs and consistency in top-level function calls by @cadeduckworth in #263
• initialize guess_atoms function PR by @cadeduckworth in #264
• Black formatting by @a-ws-m in #269
• remove logger for SI in mdpow.fep by @VOD555 in #276
• Use OOP forcefields by @a-ws-m in #267
• replace scipy.integrate.simps with simpson by @orbeckst in #282
• update versioneer by @orbeckst in #287
• Update .readthedocs.yaml by @orbeckst in #284
• change Python support to 3.10 - 3.12 by @orbeckst in #290
• auto-deploy GHA workflow by @orbeckst in #292
• Fix stage checking by @a-ws-m in #278

New Contributors

• @a-ws-m made their first contribution in #269

Full Changelog: release-0.8.0...release-0.9.0

release 0.9.0 (release candidate 3)

Pre-release for the new 0.9.0

• new features (dihedral ensemble analysis workflow)
• dropping support for old Python versions (sorry, too difficult to maintain and keep up with the Python eco system)
• GROMACS 4.6.5 to 2024.3 tested

What's Changed

• change Python support to 3.10 - 3.12 by @orbeckst in #290
• auto-deploy GHA workflow by @orbeckst in #292
• changed dihedral atom group selection strings in test_dihedral.py by @cadeduckworth in #218
• CI updates by @orbeckst in #220
• Update em_charmm.mdp by @VOD555 in #210
• use new micro mamba action by @orbeckst in #221
• developing back end run methods by @cadeduckworth in #216
• Support toluene solvent by @VOD555 in #224
• Support cgenff toluene by @VOD555 in #228
• Fix setup and support toluene in mdpow-solvationenergy by @VOD555 in #230
• Use AutoMBAR instead of MBAR by @VOD555 in #234
• Automated Dihedral Analysis by @cadeduckworth in #217
• Periodic Angle Padding by @cadeduckworth in #242
• Workflows Base Module by @cadeduckworth in #229
• update banner logging by @orbeckst in #247
• Update statistical inefficiency calculation with statistical_inefficiency in alchemlyb 2.1.0 by @VOD555 in #250
• drop python 3.7 and testing improvements by @orbeckst in #249
• test on GROMACS 2022 and 2023 by @orbeckst in #255
• use relative imports inside MDPOW by @orbeckst in #257
• update to mamba-org/setup-micromamba by @orbeckst in #258
• Dihedral Plots: RDKit Mol Object by @cadeduckworth in #243
• Review all kwargs and consistency in top-level function calls by @cadeduckworth in #263
• initialize guess_atoms function PR by @cadeduckworth in #264
• Black formatting by @a-ws-m in #269
• remove logger for SI in mdpow.fep by @VOD555 in #276
• Use OOP forcefields by @a-ws-m in #267
• replace scipy.integrate.simps with simpson by @orbeckst in #282
• update versioneer by @orbeckst in #287
• Update .readthedocs.yaml by @orbeckst in #284

New Contributors

• @a-ws-m made their first contribution in #269

Full Changelog: release-0.8.0...release-0.9.0rc3

release 0.9.0 (release candidate 1)

Pre-release for the new 0.9.0

• new features (dihedral ensemble analysis workflow)
• dropping support for old Python versions (sorry, too difficult to maintain and keep up with the Python eco system)

What's Changed

• changed dihedral atom group selection strings in test_dihedral.py by @cadeduckworth in #218
• CI updates by @orbeckst in #220
• Update em_charmm.mdp by @VOD555 in #210
• use new micro mamba action by @orbeckst in #221
• developing back end run methods by @cadeduckworth in #216
• Support toluene solvent by @VOD555 in #224
• Support cgenff toluene by @VOD555 in #228
• Fix setup and support toluene in mdpow-solvationenergy by @VOD555 in #230
• Use AutoMBAR instead of MBAR by @VOD555 in #234
• Automated Dihedral Analysis by @cadeduckworth in #217
• Periodic Angle Padding by @cadeduckworth in #242
• Workflows Base Module by @cadeduckworth in #229
• update banner logging by @orbeckst in #247
• Update statistical inefficiency calculation with statistical_inefficiency in alchemlyb 2.1.0 by @VOD555 in #250
• drop python 3.7 and testing improvements by @orbeckst in #249
• test on GROMACS 2022 and 2023 by @orbeckst in #255
• use relative imports inside MDPOW by @orbeckst in #257
• update to mamba-org/setup-micromamba by @orbeckst in #258
• Dihedral Plots: RDKit Mol Object by @cadeduckworth in #243
• Review all kwargs and consistency in top-level function calls by @cadeduckworth in #263
• initialize guess_atoms function PR by @cadeduckworth in #264
• Black formatting by @a-ws-m in #269
• remove logger for SI in mdpow.fep by @VOD555 in #276
• Use OOP forcefields by @a-ws-m in #267
• replace scipy.integrate.simps with simpson by @orbeckst in #282
• update versioneer by @orbeckst in #287
• Update .readthedocs.yaml by @orbeckst in #284

New Contributors

• @a-ws-m made their first contribution in #269

Full Changelog: release-0.8.0...release-0.9.0rc1

Release 0.8.0

New release of MDPOW with new functionality; dropped support for legacy Python versions.

Important changes and fixes

• support Python 3.7 – 3.9 (3.10 probably works but is currently not tested)
• new ensemble analysis framework (#168) with two ensemble tools
  • dihedral analysis #190
  • solvation shell analysis #195
• removed deprecated mdpow-ghyd script: use mdpow-solvationenergy (#183)
• various fixes in the config file parser

All changes

See the CHANGES file for release 0.8.0.

Release 0.7.1

Important bug fixes and documentation updates

• fixes installation issues with Python 2.7 due to alchemlyb update
• fixed some of the mdpow scripts failing
• fixed the fep.p_transfer() function
• additional online documentation for the runinput file, forcefield handling, and for the contents of the doc/examples directory in the form of docs/examples/README.rst

See CHANGES for more details.

Release 0.7.0

Major release of MDPOW as used for SAMPL7, see

• Precise force-field-based calculations of octanol-water partition coefficients for the SAMPL7 molecules. Shujie Fan, Hristo Nedev,  Ranjit Vijayan, Bogdan I. Iorga, Oliver Beckstein. Journal of Computer-Aided Molecular Design 2021, doi: 10.1007/s10822-021-00407-4
• Becksteinlab/SAMPL7_logP_data

The package was renamed from "POW" to "MDPOW". Install with

pip install mdpow

Supported platforms

• Python 2.7 and Python 3.6–3.9
• GROMACS 4.6.5, 2018, 2020, 2021 (tested and confirmed), 5, 2016, 2019 (should work)
• Linux and macOS (tested), Windows (might work)

Highlights

For details see CHANGES

• uses alchemlyb estimators by default (MBAR, BAR, TI); old MDPOW TI is still available; difference between estimators is small (see DOI 10.1007/s10822-019-00267-z)
• support CHARMM/CGENFF and AMBER forcefields (including prm files)
• new "wet octanol" solvent type (see DOI 10.1007/s10822-019-00267-z)

Release 0.6.1

Bug fix release.

• works with Gromas 4.6.x, 5.1.x, 2016.x (just source your preferred GMXRC)
• bug fixes (see CHANGES for details)
• improved tests
• internally, we use EDR files as the primary storage format for energy data; XVG.bz2 files are generated when needed but this should not affect users

Release 0.6.0

Major update since 0.5.1 with a lot of new functionality and backwards incompatible changes (eg the runinput file format was changed but a conversion script is available).