GitLab

* Overhaul benchmarking script to add lots of new features

* Added another example

* Attempt at fixing failing pypy build

* Try using mambaforge

* Debugging

* A different approach to using mambaforge

* Try a separate environment file for pypy

* copy opc ions and opc*standard.xml from https://github.com/openmm/openmmforcefields/commit/b12c2e871b60275a10b3f8f56dfc2f6d5447591f

* auto-merged files

* move charges to residue definition

* remove unmerged files

* add docs

* rename U to U4+

* rename Ag+, Tl+, Gd3+ and I- residue names

* fix O-H bond length typo

* add opc3 constraints test

This initialization is needed to prevent segfault during object destruction in certain circumstances (e.g., when a `Force` is changed before calling `Context.reinitialize()` and this change causes the corresponding `ForceImpl` to throw an exception).

Fix #3790: Collision rate for MTS BAOAB Langevin integrator now correctly accounts for number of substeps (#3791)

* Fix #3790: Collision rate for MTS BAOAB Langevin integrator now correctly accounts for number of substeps. Fix suggested by Charlie Matthews (@c-matthews)

* Fix computation of total number of substeps

* Add test for MTS friction

* Fix typo

* Fix yet another typo

* Fix typo and check against analytical result

* Fix typo

* Fix typos

* Fix more typos

* Integrate MTSLangevinIntegrator for longer to allow thermalization

* Revert number of integrator steps

* Update TestIntegrators.py

Fixed a failing test case
Co-authored-by: Peter Eastman <peter.eastman@gmail.com>

Parallelize fitting 3D splines

Updated documentation on combining multiple force field files

Added a link to the manual section describing vsite types

* Ensure valid atom order after loading a checkpoint

* Run CI builds on Python 3.11

* add guide for dev builds

* hosted env file for openmm-8 beta

* explain how to host an env

* add a namespace to support different os

* pin all the versions

* add version pins and env name

* Added pytest

* update envs

* add guide for dev builds

* hosted env file for openmm-8 beta

* explain how to host an env

* add a namespace to support different os

* pin all the versions

* add version pins and env name

* Added pytest

* Updated version number to 8.0

* add guide for dev builds

* hosted env file for openmm-8 beta

* explain how to host an env

* add a namespace to support different os

* add swm4-ndp water to addSolvent

* add equilibrated box

* typo of water radius

* fixed addSolvent description

* add swm4 to tests

* update modeller.addSolvent docstring

* update docstring for modeller.addSolvent