GitLab

* Add benchmarks from Amber20 benchmark suite to standard benchmark script

* Add ensemble option; don't change hydrogen mass in amber input files

* Download and extract .tar.gz using pure python code, no wget/tar dependencies

* Rename amber tests

* add opc and opc3 models

* update to match https://bioinformatics.cs.vt.edu/~izadi/OPC_Gromacs/opc.top



* opc box, converted from ambertools-22.0-py38h6177452_1/dat/leap/lib/opcbox.off

* change values to make serialized system match one created from prmtop as close as possible

* unit test for opc water

* opc - final values, match frcmod.opc; derivation in comments

* opc3 water - final values, shows derivation

* opc3box made from ambertools 22 dat/leap/lib/opc3box.off

* add opc3 water test

* add opc and opc3 to docs

* move tests to TestForceField.py

* move opc tests out of amoeba tests, oops

* move opcbox and opc3box pdb files
Co-authored-by: Alex Izvorski <alex@genesistherapeutics.ai>

* ZeroDivisionError Fix to Metadynamics Bias

* Corrected Error Message

* Avoid adding duplicate exclusions to CustomNonbondedForce

* Fixed error in adding explicit constraints

* Added temperature adjustment to MC barostat for simulated tempering

fixes #3612

* Added test for simulated tempering with MC barostat.

* Fixed typo in TestSimulatedTempering.py

* Updated NPT test for SimulatedTempering

* Updated variable naming

* Reverted back to harmonic oscillator test

* Added FAQ links to error messages

* Added missing Windows export

* Fix #3557 : Generate more informative error message if residue template not found.

* Fix test failures

* computeDrudeTemperature

* cleanup

* revert drude temperature computation in DrudeNoseHoover

* Do not add constraints involving extra particles

* Added test case

* Max Drude distance defaults to 0.2 nm

* Fixed incorrect number in docs

* Fixed a test case

* Access atom element field

* Update GB-Neck2 force regression test

* Use importlib_metadata instead of pkg_resources

* Use built in importlib when available

* Revert change that didn't work

* Ensure bond lengths are set before creating forces that depend on them

* Minor formatting

* Only call set switching function/distance on nonbonded force(s)

* Also catch CustomNonbondedForce

* Fix logic around setEwaldErrorTolerance

* DrudeLangevinIntegrator has getSystemTemperature()

* DrudeNoseHooverIntegrator has getSystemTemperature()

* StateDataReporter reports system temperature for Drude systems

* Fixed incorrect return type

* Add library path with os.add_dll_directory()

* Update path for Visual Studio

* Improved handling of CRYST1 records #3446

* Apply suggestions from code review
Co-authored-by: Jason Swails <jason@entos.ai>
Co-authored-by: Jason Swails <jason@entos.ai>

* Reference implementation of computed values for CustomNonbondedForce

* CPU implementation of computed values for CustomNonbondedForce

* Common implementation of computed values for CustomNonbondedForce

* Serialization of computed values

* ForceField supports computed values

Without this restriction, the compilation fails if the project folder has parent folders called "tests", "internal" or other words in these generic patterns.

* Support prmtop files created by chamber

* Support CHARMM CMAP flags

* Changed handling of SCEE and SCNB scale factors

* Add Fortran type translation for `long long`

* Replaced tabs with spaces
Co-authored-by: Peter Eastman <peter.eastman@gmail.com>