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Josh Horton 909d29ad25 Plain MD restart support (#1884) 
* split md protocol to setup and simulate, add restart support

* allow for resume in any stage

* add a single run dynamics function

* update restart to only look for checkpoints, split out remaining step logic, update tests

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Co-authored-by: Irfan Alibay <IAlibay@users.noreply.github.com>
2026-04-27 16:04:28 +01:00
..
alchemical_network_planning.rst
Merge branch 'main' into more_api_refs
2023-08-29 14:20:35 +10:00
atom_mappers.rst
expose KartografAtomMapper alongside other AtomMappers (#1751)
2025-12-16 15:38:45 -08:00
defining_and_executing_simulations.rst
docs: create quickrun execution page
2024-04-10 09:57:15 +01:00
index.rst
make CLI starting guide easier to find from the landing page (#1787)
2026-01-26 12:27:08 -08:00
ligand_network.rst
docs: add openmm_md protocol page stub
2024-02-15 13:10:12 +00:00
openmm_binding_afe.rst
Turn AFE protocols into multiple units (#1776)
2026-01-22 13:38:57 +00:00
openmm_md.rst
Plain MD restart support (#1884)
2026-04-27 16:04:28 +01:00
openmm_protocol_settings.rst
Fixing various typos (#1882)
2026-03-19 18:11:03 -07:00
openmm_rfe.rst
update docs for multiple protocol units (#1793)
2026-01-16 16:00:27 +00:00
openmm_septop.rst
Add Analysis unit for Septop (#1937)
2026-04-24 10:00:06 +01:00
openmm_solvation_afe.rst
Turn AFE protocols into multiple units (#1776)
2026-01-22 13:38:57 +00:00
systems_and_components.rst
update systems and components docs for completeness (#1954)
2026-04-24 13:17:31 +02:00