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2020-03-16	Christian Blau	Remove dysfunctional QMMM interface pt3	commit \| commitdiff \| tree
2020-03-05	Christian Blau	Add function calls to MdModules to sign up for notifications	commit \| commitdiff \| tree
2020-02-25	Christian Blau	Document density-fit cross-correlation in .mdp options	commit \| commitdiff \| tree
2019-12-12	Christian Blau	Densityfitting - enforce similarity increase with adaptive...	commit \| commitdiff \| tree
2019-12-02	Christian Blau	Relax test tolerance for cross correlation measure...	commit \| commitdiff \| tree
2019-11-07	Christian Blau	Stochastic dynamics - document that nsttcouple is ignored	commit \| commitdiff \| tree
2019-10-22	Christian Blau	Fix nst in density-fitting module	commit \| commitdiff \| tree
2019-10-18	Christian Blau	Basic refactoring genion and adding test	commit \| commitdiff \| tree
2019-10-18	Christian Blau	Adaptive force scaling for densityfitting	commit \| commitdiff \| tree
2019-09-22	Christian Blau	Add cross-correlation as density simlarity measure	commit \| commitdiff \| tree
2019-09-13	Paul Bauer	Fix nightly failures	commit \| commitdiff \| tree
2019-09-13	Christoph Junghans	cmake: add option to install legacy headers	commit \| commitdiff \| tree
2019-09-11	Christian Blau	Add comments to grompp generated .mdp output for densityfitting	commit \| commitdiff \| tree
2019-09-11	Christian Blau	End to end test for density fitting	commit \| commitdiff \| tree
2019-09-11	Christian Blau	Densityfitting write int64_t indices instead of gmx...	commit \| commitdiff \| tree
2019-09-10	Christian Blau	Use the current mass instead of massA in density fitting...	commit \| commitdiff \| tree
2019-09-10	Christian Blau	Account for reference density origin shift in pbc correction	commit \| commitdiff \| tree
2019-09-09	Christian Blau	Add option to normalize densities prior to density...	commit \| commitdiff \| tree
2019-09-06	Christian Blau	Periodic boundary correction for density fitting	commit \| commitdiff \| tree
2019-09-04	Christian Blau	Fix double overload in LocalAtomSet code when gmx:...	commit \| commitdiff \| tree
2019-08-25	Christian Blau	Index groups for MdModules from grompp	commit \| commitdiff \| tree
2019-08-15	Christian Blau	Move densityfitting options and output into seperate...	commit \| commitdiff \| tree
2019-08-15	Berk Hess	Template bonded interactions on kernel flavor	commit \| commitdiff \| tree
2019-08-13	Artem Zhmurov	Make use of reference data in integrator tests	commit \| commitdiff \| tree
2019-08-13	Artem Zhmurov	Make use of reference data in SETTLE tests	commit \| commitdiff \| tree
2019-08-09	Paul Bauer	Add conversion from legacy to modern matrix type	commit \| commitdiff \| tree
2019-08-08	Christian Blau	Provide callbacks/notifications for MDModules	commit \| commitdiff \| tree
2019-08-06	Artem Zhmurov	Remove PImpl scaffolding from CUDA version of Leap...	commit \| commitdiff \| tree
2019-08-06	Berk Hess	Add ForceWithShiftForces class	commit \| commitdiff \| tree
2019-08-06	Berk Hess	Fix latex formula in reference manual	commit \| commitdiff \| tree
2019-08-06	M. Eric Irrgang	Resolve a compiler warning for the gmxapi Python package.	commit \| commitdiff \| tree
2019-08-05	Mark Abraham	Add quote	commit \| commitdiff \| tree
2019-08-05	Berk Hess	Make box const in do_force()	commit \| commitdiff \| tree
2019-08-05	Paul Bauer	Add replacements for pbc enumerations	commit \| commitdiff \| tree
2019-08-05	Paul Bauer	Add free function to convert matrix type	commit \| commitdiff \| tree
2019-07-25	Kevin Boyd	Add transpose operation to Matrix3x3	commit \| commitdiff \| tree
2019-07-24	Christian Blau	Fix HTML source documenation error caused by GaussTransform3D	commit \| commitdiff \| tree
2019-07-24	M. Eric Irrgang	Begin new sample_restraint development.	commit \| commitdiff \| tree
2019-07-18	M. Eric Irrgang	Improve some documentation formatting and spelling.	commit \| commitdiff \| tree
2019-07-18	M. Eric Irrgang	Remove extraneous file.	commit \| commitdiff \| tree
2019-07-18	Paul Bauer	Extend MDLogger levels	commit \| commitdiff \| tree
2019-07-17	Paul Bauer	Move methods out from trjconv	commit \| commitdiff \| tree
2019-07-03	Mark Abraham	Reorder options	commit \| commitdiff \| tree
2019-06-28	Christian Blau	Add class to look up density fitting amplitudes	commit \| commitdiff \| tree
2019-06-20	Christian Blau	Add coordinate scaling class and extend TranslateAndScale	commit \| commitdiff \| tree
2019-06-20	Christian Blau	Allow non-uniform Gaussians	commit \| commitdiff \| tree
2019-06-18	Paul Bauer	Extend ISerializer functionality	commit \| commitdiff \| tree
2019-05-08	Mark Abraham	Provide hook for forks of GROMACS to describe themselves	commit \| commitdiff \| tree
2019-04-22	Christian Blau	Three dimensional gauss transform	commit \| commitdiff \| tree
2019-04-22	Christian Blau	One dimensional Gaussian function on lattice.	commit \| commitdiff \| tree
2019-03-25	Mark Abraham	Support ArrayRef of EnumerationArray	commit \| commitdiff \| tree
2019-03-25	M. Eric Irrgang	Remove uses of std::iterator mix-in.	commit \| commitdiff \| tree
2019-03-22	Paul Bauer	Add simple tests for symbol table	commit \| commitdiff \| tree
2019-03-20	Paul Bauer	Add simple test to preprocess bond atom type	commit \| commitdiff \| tree
2019-03-20	Paul Bauer	Add test for string comparison	commit \| commitdiff \| tree
2019-03-19	Mark Abraham	Add support for serializing 32-bit integers	commit \| commitdiff \| tree
2019-03-19	Christian Blau	densityfitting - density file format (mrc) header.	commit \| commitdiff \| tree
2019-03-19	Paul Bauer	Fix case insensitive string comparison	commit \| commitdiff \| tree
2019-03-19	Mark Abraham	Fix clang warning	commit \| commitdiff \| tree
2019-03-19	Mark Abraham	Update ElectricField module	commit \| commitdiff \| tree
2019-03-13	Paul Bauer	Add tests for preprocess atom types	commit \| commitdiff \| tree
2019-03-13	Paul Bauer	Refactor t_param to InteractionType	commit \| commitdiff \| tree
2019-03-08	Paul Bauer	Refactor preprocessing atom types.	commit \| commitdiff \| tree
2019-03-07	Mark Abraham	New tests for pdb2gmx and editconf	commit \| commitdiff \| tree
2019-03-06	Paul Bauer	Add error when manual cannot be built	commit \| commitdiff \| tree
2019-02-27	Mark Abraham	Keep niche CMake variables as advanced	commit \| commitdiff \| tree
2019-02-25	Mark Abraham	Move code out of sim_util.cpp	commit \| commitdiff \| tree
2019-02-15	Paul Bauer	Fix memory leaks in editconf	commit \| commitdiff \| tree
2019-02-14	Mark Abraham	Fix use of selections referring to index groups	commit \| commitdiff \| tree
2019-02-14	Mark Abraham	Revert changes to implementation of insert-molecules...	commit \| commitdiff \| tree
2019-02-13	Paul Bauer	Refactor rtp renaming	commit \| commitdiff \| tree
2019-02-13	Mark Abraham	Make EnergyOutput wrapper class	commit \| commitdiff \| tree
2019-02-08	Mark Abraham	Remove copy_energy from energy-writing steps	commit \| commitdiff \| tree
2019-02-07	Roland Schulz	Add ssize and remove static_casts	commit \| commitdiff \| tree
2019-01-25	Mark Abraham	Unify regex implementation	commit \| commitdiff \| tree
2019-01-24	Christian Blau	Remove extra semicolons causing clang warnings.	commit \| commitdiff \| tree
2019-01-18	Kevin Boyd	Add tests for gmx mindist	commit \| commitdiff \| tree
2018-12-20	David van der Spoel	Removed t_topology from gmx msd	commit \| commitdiff \| tree
2018-12-12	Szilárd Páll	Improve DLB report/note	commit \| commitdiff \| tree
2018-12-10	Paul Bauer	Use more const references in topology code	commit \| commitdiff \| tree
2018-12-06	boristim	Updates to do_dssp	commit \| commitdiff \| tree
2018-10-03	Mark Abraham	Basic modernization of md5 handling	commit \| commitdiff \| tree
2018-08-30	Christian Blau	Convert essential dynamics C-structs to C++ pt1.	commit \| commitdiff \| tree
2018-08-20	Berk Hess	Make gmx_ga2la_t a proper class	commit \| commitdiff \| tree
2018-08-17	Berk Hess	Make pull pbc atom use LocalAtomSet	commit \| commitdiff \| tree
2018-08-14	Roland Schulz	Remove BasicVector.as_vec	commit \| commitdiff \| tree
2018-08-10	Kevin Boyd	Added physical validation document to the dev manual.	commit \| commitdiff \| tree
2018-08-09	Christian Blau	Remove Debug Helpers from Essential Dynamics code.	commit \| commitdiff \| tree
2018-08-08	Christian Blau	Essential dynamics functions use const-ref for input...	commit \| commitdiff \| tree
2018-08-08	Christian Blau	Split essential dynamics eigenvector reading.	commit \| commitdiff \| tree
2018-08-08	Christian Blau	Make essential dynamics a C++ type.	commit \| commitdiff \| tree

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