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2018-06-06	Berk Hess	Clean up make_at2con	commit \| commitdiff \| tree
2018-06-05	Berk Hess	Make nbnxn_grid_t counts and sizes arrays	commit \| commitdiff \| tree
2018-05-24	Berk Hess	Fix grompp bug with blocks of same molecules	commit \| commitdiff \| tree
2018-05-24	Berk Hess	Simplify idef_fe in calc_listed_lambda	commit \| commitdiff \| tree
2018-05-24	Berk Hess	Change nbs in nbv to std::unique	commit \| commitdiff \| tree
2018-05-24	Berk Hess	Convert gmx_domdec_master_t to C++	commit \| commitdiff \| tree
2018-05-23	Berk Hess	Split off collect.cpp from domdec.cpp	commit \| commitdiff \| tree
2018-05-23	Berk Hess	Convert nbnxn_search to C++	commit \| commitdiff \| tree
2018-05-22	Berk Hess	Change nbnxn grid reallocation	commit \| commitdiff \| tree
2018-05-22	Berk Hess	Use std::vector in nbnxn_search_t	commit \| commitdiff \| tree
2018-05-22	Berk Hess	Use std::vector in nbnxn_grid_t	commit \| commitdiff \| tree
2018-05-18	Berk Hess	Clean up in nbnxn_grid.cpp	commit \| commitdiff \| tree
2018-05-17	Berk Hess	Split off domdec distribution and cellsizes	commit \| commitdiff \| tree
2018-05-17	Berk Hess	Split atom redistribution off from domdec.cpp	commit \| commitdiff \| tree
2018-05-17	Berk Hess	Remove commrec from set_ddbox()	commit \| commitdiff \| tree
2018-05-15	Berk Hess	Clean up PME domain count passing	commit \| commitdiff \| tree
2018-05-03	Berk Hess	Enable SIMD version of update	commit \| commitdiff \| tree
2018-04-27	Berk Hess	Remove pull MPI code duplication	commit \| commitdiff \| tree
2018-04-24	Berk Hess	Fix indexing issue in the pull code	commit \| commitdiff \| tree
2018-04-16	Berk Hess	Move natoms_mol out of gmx_molblock_t	commit \| commitdiff \| tree
2018-04-09	Berk Hess	Convert gmx_molblock_t to C++	commit \| commitdiff \| tree
2018-04-03	Berk Hess	Convert gmx_mtop_t to C++	commit \| commitdiff \| tree
2018-04-03	Berk Hess	Change warninp filenm to std::string	commit \| commitdiff \| tree
2018-04-03	Berk Hess	Do not calculate COM for pull group 0	commit \| commitdiff \| tree
2018-03-29	Berk Hess	Move file opening out of init_pull()	commit \| commitdiff \| tree
2018-03-29	Berk Hess	Modularize pull_coord_work_t	commit \| commitdiff \| tree
2018-03-28	Berk Hess	Remove mols from gmx_mtop_t	commit \| commitdiff \| tree
2018-03-20	Berk Hess	Fix gmx dump AWH formatting issue	commit \| commitdiff \| tree
2018-03-20	Berk Hess	Disallow single simulation with multisim	commit \| commitdiff \| tree
2018-03-16	Berk Hess	Correct PMF sign error in AWH bias sharing	commit \| commitdiff \| tree
2018-03-16	Berk Hess	Fix recent mdrun signaling bug	commit \| commitdiff \| tree
2018-03-15	Berk Hess	Fix virial with external pull potential and MPI	commit \| commitdiff \| tree
2018-03-14	Berk Hess	Improve inter-simulation signaling	commit \| commitdiff \| tree
2018-03-14	Berk Hess	Fix mdrun signalling with AWH bias sharing	commit \| commitdiff \| tree
2018-03-14	Berk Hess	Fix COM pulling with external potential with #ranks>32	commit \| commitdiff \| tree
2018-03-14	Berk Hess	Fix pull bug with geometry=direction-periodic	commit \| commitdiff \| tree
2018-03-13	Berk Hess	Add AWH fixes to release notes	commit \| commitdiff \| tree
2018-03-13	Berk Hess	Fix AWH ensemble checkpointing	commit \| commitdiff \| tree
2018-03-13	Berk Hess	Fix AWH deconvolution when sharing a bias	commit \| commitdiff \| tree
2018-03-09	Berk Hess	Correct pdb2gmx -missing option	commit \| commitdiff \| tree
2018-03-07	Berk Hess	Fix memory leak in PME	commit \| commitdiff \| tree
2018-03-06	Berk Hess	Convert t_filenm to C++	commit \| commitdiff \| tree
2018-03-06	Berk Hess	Make multi-atom TPI reproducible	commit \| commitdiff \| tree
2018-03-05	Berk Hess	Work around gcc bug with group kernel tables	commit \| commitdiff \| tree
2018-03-05	Berk Hess	Leave nullptr opt in t_filenm	commit \| commitdiff \| tree
2018-03-02	Berk Hess	Fix cppcheck warning	commit \| commitdiff \| tree
2018-03-02	Berk Hess	Fix AWH bias-sharing with parallel simulation	commit \| commitdiff \| tree
2018-03-01	Berk Hess	Detect AMD SMT topology	commit \| commitdiff \| tree
2018-03-01	Berk Hess	Fix mdrun multisim with separate PME ranks	commit \| commitdiff \| tree
2018-02-23	Berk Hess	Fix md integrator with Nose-Hoover coupling	commit \| commitdiff \| tree
2018-02-22	Berk Hess	Simplify mdrun tMPI thread spawning	commit \| commitdiff \| tree
2018-02-16	Berk Hess	Correct multisim MPI barrier	commit \| commitdiff \| tree
2018-02-14	Berk Hess	Remove support for tpx version before 58/gmx4.0	commit \| commitdiff \| tree
2018-02-14	Berk Hess	Fix range bug in add_selection_groups in tngio.cpp	commit \| commitdiff \| tree
2018-02-14	Berk Hess	Fix grompp net charge check	commit \| commitdiff \| tree
2018-02-14	Berk Hess	Fix grompp net charge check	commit \| commitdiff \| tree
2018-02-08	Berk Hess	Use SIMD bondeds without perturbed interactions	commit \| commitdiff \| tree
2018-02-08	Berk Hess	Allow bonds with distance=0	commit \| commitdiff \| tree
2018-02-05	Berk Hess	Set cutoff modifiers in forcerec	commit \| commitdiff \| tree
2018-02-05	Berk Hess	Fix assertion failure in TPI	commit \| commitdiff \| tree
2018-01-30	Berk Hess	Removed unused flag PCA_CAN_READ_NODE	commit \| commitdiff \| tree
2018-01-18	Berk Hess	Fix COMM removal on part of the system	commit \| commitdiff \| tree
2018-01-18	Berk Hess	Add check in grompp to avoid assertion failure	commit \| commitdiff \| tree
2018-01-17	Berk Hess	Replace stderr prints in filenm.cpp by asserts	commit \| commitdiff \| tree
2018-01-17	Berk Hess	Re-enable GPU with walls and 1 energy group	commit \| commitdiff \| tree
2018-01-16	Berk Hess	Remove tumbling ice-cube warning with SD	commit \| commitdiff \| tree
2018-01-16	Berk Hess	Avoid mdrun echoing "No option -multi"	commit \| commitdiff \| tree
2018-01-09	Berk Hess	Reword CPU/GPU imbalance notes	commit \| commitdiff \| tree
2018-01-09	Berk Hess	Do not turn on DLB at replica exchange	commit \| commitdiff \| tree
2018-01-08	Berk Hess	Fix triclinic domain decomposition bug	commit \| commitdiff \| tree
2017-12-19	Berk Hess	Make acceleration correction VCM mode work	commit \| commitdiff \| tree
2017-12-19	Berk Hess	Make oversubscription warning consistent	commit \| commitdiff \| tree
2017-12-14	Berk Hess	Require -ntmpi with setting -ntomp with GPUs	commit \| commitdiff \| tree
2017-12-12	Berk Hess	Check for large energy at first step	commit \| commitdiff \| tree
2017-12-12	Berk Hess	Avoid yelling about thread pinning twice	commit \| commitdiff \| tree
2017-12-11	Berk Hess	Add grompp note for PR pcouple + position restraints	commit \| commitdiff \| tree
2017-12-10	Berk Hess	Remove SIMD warning for AMD Zen	commit \| commitdiff \| tree
2017-12-10	Berk Hess	Tone down note about not pinning threads	commit \| commitdiff \| tree
2017-12-08	Berk Hess	Correct Shake test tolerances	commit \| commitdiff \| tree
2017-12-08	Berk Hess	Add Viveca Lindahl as contributor	commit \| commitdiff \| tree
2017-12-07	Berk Hess	Choose faster nbnxn SIMD kernels on AMD Zen	commit \| commitdiff \| tree
2017-12-05	Berk Hess	Fix DD exact continuation bug	commit \| commitdiff \| tree
2017-12-04	Berk Hess	Fix pme gather in double with AVX(2)_128	commit \| commitdiff \| tree
2017-12-04	Berk Hess	Merge "Merge branch release-2016 into release-2018...	commit \| commitdiff \| tree
2017-12-04	Berk Hess	Fixed initial temperature reporting	commit \| commitdiff \| tree
2017-12-04	Berk Hess	Update mdrun signal help text	commit \| commitdiff \| tree
2017-12-04	Berk Hess	Only stop at nstlist steps with -reprod	commit \| commitdiff \| tree
2017-12-03	Berk Hess	Clear vsite velocities for simple integrators	commit \| commitdiff \| tree
2017-12-03	Berk Hess	Tighten B-spline moduli single precision test tolerance...	commit \| commitdiff \| tree
2017-12-02	Berk Hess	Avoid assertion failure in AWH	commit \| commitdiff \| tree
2017-11-29	Berk Hess	Change the GPU SMT cut-off to quadratic	commit \| commitdiff \| tree
2017-11-28	Berk Hess	Update documention of Nose-Hoover output	commit \| commitdiff \| tree
2017-11-28	Berk Hess	Refactor nbnxn exclusion setting	commit \| commitdiff \| tree
2017-11-28	Berk Hess	Extend grompp missing energy term message	commit \| commitdiff \| tree
2017-11-27	Berk Hess	Enable auto thread pinning with thread limiting	commit \| commitdiff \| tree
2017-11-27	Berk Hess	Fix PME GPU with walls	commit \| commitdiff \| tree
2017-11-25	Berk Hess	Fix compiler warning without MPI	commit \| commitdiff \| tree
2017-11-24	Berk Hess	Disabled CUDA timings	commit \| commitdiff \| tree
2017-11-24	Berk Hess	Speed up nbnxn buffer clearing	commit \| commitdiff \| tree
2017-11-24	Berk Hess	Limit SMT with PME on GPU	commit \| commitdiff \| tree
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