Implemented QM/MM workflow inside core GROMACS
commit1113f056319750c05503c4b965e49b5eb0bd85c1
authorViacheslav Bolnykh <bolnykh@gmail.com>
Fri, 5 Jan 2018 17:16:44 +0000 (5 18:16 +0100)
committerMark Abraham <mark.j.abraham@gmail.com>
Fri, 12 Oct 2018 08:34:43 +0000 (12 10:34 +0200)
tree3d0c4a157650d6b6fde1a1bb7183199b886f8821
parent6f025f6e954959606e889abbee0617dce7bdaca6
Implemented QM/MM workflow inside core GROMACS

Implemented MiMiC integrator along with the generation of
inter-molecular exclusion lists for QM atoms both in serial and parallel
parts of the code

Fixes #2309

Change-Id: I35073ad69752e22968c0e2821e2fdf9f0c465b2a
34 files changed:
CMakeLists.txt
docs/doxygen/cycle-suppressions.txt
docs/install-guide/index.rst
docs/user-guide/mdp-options.rst
src/gromacs/CMakeLists.txt
src/gromacs/domdec/domdec_topology.cpp
src/gromacs/mdrun/CMakeLists.txt
src/gromacs/mdrun/integrator.cpp
src/gromacs/mdrun/integrator.h
src/gromacs/mdrun/mimic.cpp [copied from src/gromacs/mdrun/rerun.cpp with 71% similarity]
src/gromacs/mdrun/mimic.h [copied from src/gromacs/mdrun/integrator.cpp with 53% similarity]
src/gromacs/mdrun/rerun.cpp
src/gromacs/mimic/CMakeLists.txt [copied from src/gromacs/mdrun/CMakeLists.txt with 84% similarity]
src/gromacs/mimic/MimicCommunicator.cpp [new file with mode: 0644]
src/gromacs/mimic/MimicCommunicator.h [new file with mode: 0644]
src/gromacs/mimic/MimicUtils.cpp [copied from src/gromacs/mdrun/integrator.cpp with 52% similarity]
src/gromacs/mimic/MimicUtils.h [copied from src/gromacs/mdrun/integrator.cpp with 51% similarity]
src/gromacs/topology/mtop_util.cpp
src/gromacs/topology/mtop_util.h
src/gromacs/topology/topology.h
src/programs/mdrun/tests/1quantum.ndx [new file with mode: 0644]
src/programs/mdrun/tests/2quantum.ndx [new file with mode: 0644]
src/programs/mdrun/tests/4water.gro [new file with mode: 0644]
src/programs/mdrun/tests/4water.top [new file with mode: 0644]
src/programs/mdrun/tests/CMakeLists.txt
src/programs/mdrun/tests/ala.gro [new file with mode: 0644]
src/programs/mdrun/tests/ala.ndx [new file with mode: 0644]
src/programs/mdrun/tests/ala.top [new file with mode: 0644]
src/programs/mdrun/tests/allquantum.ndx [new file with mode: 0644]
src/programs/mdrun/tests/mimic.cpp [new file with mode: 0644]
src/programs/mdrun/tests/refdata/MimicTest_AllQuantumMol.xml [new file with mode: 0644]
src/programs/mdrun/tests/refdata/MimicTest_BondCuts.xml [new file with mode: 0644]
src/programs/mdrun/tests/refdata/MimicTest_OneQuantumMol.xml [new file with mode: 0644]
src/programs/mdrun/tests/refdata/MimicTest_TwoQuantumMol.xml [new file with mode: 0644]