GitLab

* enable atom subset in PDBReporter

* adds optional atomSubset argument to PDBReporter
* adds functions in PDBReporter which create a new topology
  and positions with chosen subset of atoms
* PDBReporter write PDB files with the subset topology and positions.

* refactor PDBReporter

* make _createTopologySubset a method that is called only the first time it is needed
* more efficient creation of subset positions
* check that atomSubset is ordered

* refactoring PDBReporter and add PDBx

* move checks on atomSubset to _createSubsetTopology
* copy periodic box vectors from topology to subsetTopology
* add atomSubset to PDBx reporter

* add bond subset to createSubsetTopology

* formatting changes to pdbreporter

* loop over atoms cleaned up
* put file opening inside parameter loop in
  TestPdbReporter::testinvalidSubsets to try and fix failing tests on windows

* add thorough tests to TestPdbReporter

* spelling changes
* Add tests for atom positions, elements, names etc
* attempt at fixing PyPy and Windows failing test cases

* fix spellings

* close output file before raising exceptions

* closes output files before raising exception in pdbreporter
createSubsetTopology
* changes assertVecAlmostEqual from a method to function to avoid
  repeating

* 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

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>

* add swm4-ndp water to addSolvent

* add equilibrated box

* typo of water radius

* fixed addSolvent description

* add swm4 to tests

* 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>

* 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

* 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

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

* Minor formatting

* 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

* Support prmtop files created by chamber

* Support CHARMM CMAP flags

* Changed handling of SCEE and SCNB scale factors

* Added GLYCAM

* Improved tests and documentation

* Fixed incorrect external bonds

* Adding support for new AMOEBA features

* Support modern method of specifying in-plane angles

* Implemented stretch-torsions

* Implemented angle-torsions

* More AMOEBA fixes

* Bug fix

* Converted AMOEBA 2018 force field

* Added documentation for AMOEBA 2018

* Added a missing file for tests

* Improved handling of atoms with alternate locations

* Fixed a test failure caused by an invalid PDB file

* Added option for CheckpointReporter to save States

* Try to fix test failure on Windows

* Allow querying current step count

* Fixed error building Python wrapper

* Check for keyword args to createSystem() that are never used

* Fixed incorrect arguments in test cases

* Created OBC2 that works with current force fields

* Created HCT, OBC1, GBn, and GBn2 that works with current force fields

* Added documentation for GB models

* Updates to documentation and tests based on comments

* Added formula for screening parameter

* Support of Amber FF19SB CMAP

* Update: Support of Amber FF19SB CMAP
Co-authored-by: Kye Won Wang <kyw220@sol.cc.lehigh.edu>

* Replaced several AMOEBA bonded forces with custom forces

* Deleted obsolete AMOEBA forces

* Replaced AmoebaPiTorsionForce with custom force

* Top level Python module is now "openmm"

* Updated module names in examples

* Updated module names in documentation

* Updated module in CI scripts

* Added deprecation warning

* Made ordering of impropers more deterministic

* Fixed typo

* Do not alter mass of hydrogens in rigid water

* Do not alter mass of hydrogens in rigid water