Implemented changes to preprocessor to work with MiMiC QM/MM
authorViacheslav Bolnykh <bolnykh@gmail.com>
Fri, 5 Jan 2018 17:16:44 +0000 (18:16 +0100)
committerMark Abraham <mark.j.abraham@gmail.com>
Tue, 9 Oct 2018 11:50:37 +0000 (13:50 +0200)
commit61e7a6a126acd5ed6397bd90a10fa6897b094e5d
tree600dd0e2d546bc51c4d38265551ab5b6c3f663d7
parentbb939538ae00a8a85947055580c4c4c46436e6ab
Implemented changes to preprocessor to work with MiMiC QM/MM

Added new integrator "mimic" and updated usage of QMMM-grps to be used
with MiMiC QM/MM. Updated code zeros charges within QM region and
changes bonds to CONNBOND and updates exclusion lists to exclude
non-bonded interactions between quantum atoms

Refs #2308

Change-Id: I34e798ae0c54457dad8f9a8f220482468db34708
19 files changed:
CMakeLists.txt
cmake/gmxManageMimic.cmake [new file with mode: 0644]
src/config.h.cmakein
src/gromacs/fileio/tpxio.cpp
src/gromacs/gmxpreprocess/grompp.cpp
src/gromacs/gmxpreprocess/readir.cpp
src/gromacs/gmxpreprocess/tests/readir.cpp
src/gromacs/gmxpreprocess/tests/refdata/GetIrTest_HandlesMimic.xml [new file with mode: 0644]
src/gromacs/gmxpreprocess/topio.cpp
src/gromacs/gmxpreprocess/topio.h
src/gromacs/mdtypes/md_enums.cpp
src/gromacs/mdtypes/md_enums.h
src/gromacs/topology/atoms.cpp
src/gromacs/topology/block.cpp
src/gromacs/topology/block.h
src/gromacs/topology/idef.cpp
src/gromacs/topology/idef.h
src/gromacs/topology/topology.cpp
src/gromacs/topology/topology.h