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2017-09-15	Berk Hess	Remove nb-parameters from t_forcerec	commit \| commitdiff \| tree
2017-09-12	Berk Hess	Fix exception in SIMD LJ PME solve	commit \| commitdiff \| tree
2017-09-12	Berk Hess	Do not pass state to init_replica_exchange	commit \| commitdiff \| tree
2017-09-11	Berk Hess	Fix PBC bugs in the swap code	commit \| commitdiff \| tree
2017-09-09	Berk Hess	Avoid inf in SIMD double sqrt()	commit \| commitdiff \| tree
2017-09-07	Berk Hess	Fix FEP state with rerun	commit \| commitdiff \| tree
2017-09-04	Berk Hess	Fix two nbnxn search indexing bugs	commit \| commitdiff \| tree
2017-09-04	Berk Hess	Consolidate architecture booleans	commit \| commitdiff \| tree
2017-09-03	Berk Hess	Put mdrun options in structs	commit \| commitdiff \| tree
2017-09-02	Berk Hess	Put all domdec options in a struct	commit \| commitdiff \| tree
2017-09-02	Berk Hess	Fix mdrun -nb option pointer	commit \| commitdiff \| tree
2017-09-01	Berk Hess	Fix mdrun -nb option pointer	commit \| commitdiff \| tree
2017-08-29	Berk Hess	Make pull potential registration thread-safe	commit \| commitdiff \| tree
2017-08-29	Berk Hess	Set default GMX_OPENMP_MAX_THREADS to 64	commit \| commitdiff \| tree
2017-08-28	Berk Hess	Avoid bonded forces loops/timers on inputs with no...	commit \| commitdiff \| tree
2017-08-22	Berk Hess	Enable dynamic pair list pruning	commit \| commitdiff \| tree
2017-08-18	Berk Hess	Add CPU reference and SIMD pruning kernels	commit \| commitdiff \| tree
2017-08-16	Berk Hess	Add dynamic pair-list pruning framework	commit \| commitdiff \| tree
2017-08-16	Berk Hess	Clean up nbnxn cluster pair addition code	commit \| commitdiff \| tree
2017-08-15	Berk Hess	Add OpenMP for orientation restraints	commit \| commitdiff \| tree
2017-08-15	Berk Hess	Use graph with orientation restraints	commit \| commitdiff \| tree
2017-08-12	Berk Hess	Remove loop over all atoms in init_mdatoms	commit \| commitdiff \| tree
2017-08-03	Berk Hess	Fix orientation restraint reference	commit \| commitdiff \| tree
2017-08-03	Berk Hess	Add check for nr of orientation restraints	commit \| commitdiff \| tree
2017-08-03	Berk Hess	Fix bugs with orientation restraints	commit \| commitdiff \| tree
2017-08-02	Berk Hess	Clean up matrix inversion	commit \| commitdiff \| tree
2017-08-02	Berk Hess	Fix orientation restraint reference	commit \| commitdiff \| tree
2017-08-02	Berk Hess	Make loop variables in orires.cpp local	commit \| commitdiff \| tree
2017-08-02	Berk Hess	Add check for nr of orientation restraints	commit \| commitdiff \| tree
2017-07-25	Berk Hess	Fix bugs with orientation restraints	commit \| commitdiff \| tree
2017-07-09	Berk Hess	Restructure the load balancing timing	commit \| commitdiff \| tree
2017-07-04	Berk Hess	Unify nbnxn kernel dispatchers	commit \| commitdiff \| tree
2017-07-03	Berk Hess	Remove gmx_constexpr	commit \| commitdiff \| tree
2017-06-17	Berk Hess	Add tolerance to calc_verletbuf test	commit \| commitdiff \| tree
2017-06-12	Berk Hess	Disable PME tuning with the group scheme	commit \| commitdiff \| tree
2017-06-12	Berk Hess	Fix null pointer print in DD	commit \| commitdiff \| tree
2017-06-10	Berk Hess	Put replica exchange parameters in a struct	commit \| commitdiff \| tree
2017-06-09	Berk Hess	Replace iso by instead of	commit \| commitdiff \| tree
2017-06-08	Berk Hess	Fix COM pull force with SD	commit \| commitdiff \| tree
2017-06-07	Berk Hess	Avoid grompp charge warning with rounding	commit \| commitdiff \| tree
2017-06-04	Berk Hess	Fix checkpoint reading without energy history	commit \| commitdiff \| tree
2017-06-02	Berk Hess	Fix initial temperature reporting	commit \| commitdiff \| tree
2017-05-27	Berk Hess	Made duplicate atoms in bondeds an error	commit \| commitdiff \| tree
2017-05-26	Berk Hess	Improve Verlet buffer constraint estimate	commit \| commitdiff \| tree
2017-05-23	Berk Hess	Add conserved quantity for Berendsen P-couple	commit \| commitdiff \| tree
2017-05-23	Berk Hess	Add conserved q. for PR and Berendsen T-couple	commit \| commitdiff \| tree
2017-05-23	Berk Hess	Make DD setup obey PME restrictions	commit \| commitdiff \| tree
2017-05-22	Berk Hess	Introduce ObservablesHistory container	commit \| commitdiff \| tree
2017-05-16	Berk Hess	Fix confout.gro with energy minimization	commit \| commitdiff \| tree
2017-05-15	Berk Hess	Fix LJPME + switch grompp error	commit \| commitdiff \| tree
2017-05-14	Berk Hess	Fix bugs in double Simd4 implementations	commit \| commitdiff \| tree
2017-04-21	Berk Hess	Fix bugs in double AVX(2)_256 Simd4	commit \| commitdiff \| tree
2017-04-19	Berk Hess	Fix unused SIMD PME table kernel	commit \| commitdiff \| tree
2017-04-18	Berk Hess	Suppress two compiler warnings	commit \| commitdiff \| tree
2017-03-16	Berk Hess	Replace instance of group by coord in pull mdp docs	commit \| commitdiff \| tree
2017-03-14	Berk Hess	Make grompp -r obligatory with posres	commit \| commitdiff \| tree
2017-02-28	Berk Hess	Add load balance fraction to DLB print	commit \| commitdiff \| tree
2017-02-07	Berk Hess	Add mdp option check with decoupled modes	commit \| commitdiff \| tree
2017-02-02	Berk Hess	Really fix array of complex in cross_corr	commit \| commitdiff \| tree
2017-02-02	Berk Hess	Fix array of complex in cross_corr	commit \| commitdiff \| tree
2017-01-20	Berk Hess	Disallow overwriting of dihedral type 9	commit \| commitdiff \| tree
2017-01-20	Berk Hess	Only predict shells with velocities	commit \| commitdiff \| tree
2017-01-19	Berk Hess	Fix PME order and grid size checks	commit \| commitdiff \| tree
2017-01-17	Berk Hess	Correct assert on pme-order	commit \| commitdiff \| tree
2017-01-05	Berk Hess	Fix flat-bottom position restraints + DD + OpenMP	commit \| commitdiff \| tree
2016-12-14	Berk Hess	Add bonded #thread runtime check	commit \| commitdiff \| tree
2016-12-08	Berk Hess	Made mdrun -pforce terminate with non-finite forces	commit \| commitdiff \| tree
2016-11-24	Berk Hess	Change spline moduli calculation to double	commit \| commitdiff \| tree
2016-11-23	Berk Hess	Convert energyhistory_t to use std::vector	commit \| commitdiff \| tree
2016-11-23	Berk Hess	Use templating in checkpoint.cpp	commit \| commitdiff \| tree
2016-11-01	Berk Hess	Fix time label print in gmx vanhove	commit \| commitdiff \| tree
2016-10-29	Berk Hess	Add gmx dump option for printing parameters	commit \| commitdiff \| tree
2016-10-28	Berk Hess	DLB can now turn off, when slower	commit \| commitdiff \| tree
2016-10-28	Berk Hess	Fix DLB timing with CUDA and OpenCL	commit \| commitdiff \| tree
2016-10-15	Berk Hess	Move energyhistory_t out of t_state	commit \| commitdiff \| tree
2016-10-14	Berk Hess	Apply Berendsen P-couple at nstpcouple steps	commit \| commitdiff \| tree
2016-10-13	Berk Hess	Extend mtop_lookup.h	commit \| commitdiff \| tree
2016-10-12	Berk Hess	Fixed exception in usused result	commit \| commitdiff \| tree
2016-10-12	Berk Hess	Fixed print bug in gmx wham	commit \| commitdiff \| tree
2016-10-12	Berk Hess	Refactor NPT energy calculation	commit \| commitdiff \| tree
2016-10-12	Berk Hess	Restructure leap-frog integrators	commit \| commitdiff \| tree
2016-10-11	Berk Hess	Speed up mtop_util atom lookup	commit \| commitdiff \| tree
2016-10-08	Berk Hess	Add readConfAndTopology	commit \| commitdiff \| tree
2016-10-07	Berk Hess	Changed fr->f_novirsum to PaddedRVecVector	commit \| commitdiff \| tree
2016-10-01	Berk Hess	Fix inputrec initialization in 4 tools	commit \| commitdiff \| tree
2016-09-29	Berk Hess	Use std::vector in t_state	commit \| commitdiff \| tree
2016-09-29	Berk Hess	Add flags for optional t_atoms entries	commit \| commitdiff \| tree
2016-09-22	Berk Hess	Fix gcc warning in AlignedAllocator	commit \| commitdiff \| tree
2016-09-20	Berk Hess	Remove state duplication in serial runs	commit \| commitdiff \| tree
2016-09-16	Berk Hess	Fixed unused variables in domdec.cpp	commit \| commitdiff \| tree
2016-09-16	Berk Hess	Merge branch release-2016	commit \| commitdiff \| tree
2016-09-16	Berk Hess	Made distance restraints work with threads and DD	commit \| commitdiff \| tree
2016-09-13	Berk Hess	Moved expanded ensemble history to pointer in t_state	commit \| commitdiff \| tree
2016-09-13	Berk Hess	Change ED and swapstate to pointers in t_state	commit \| commitdiff \| tree
2016-09-12	Berk Hess	Add const to thread-MPI functions	commit \| commitdiff \| tree
2016-09-10	Berk Hess	Remove continuation from convert_tpr	commit \| commitdiff \| tree
2016-09-06	Berk Hess	Fix bug with conjugate-gradient and OpenMP	commit \| commitdiff \| tree
2016-09-06	Berk Hess	Consolidate MD algorithm atom setup	commit \| commitdiff \| tree
2016-09-05	Berk Hess	Re-enable flexible constraints with DD	commit \| commitdiff \| tree
2016-09-04	Berk Hess	Merge branch release-2016	commit \| commitdiff \| tree
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