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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
2017-06-07	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
2017-05-27	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
2017-04-21	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
2016-09-03	Berk Hess	Clean up PME flags variable use	commit \| commitdiff \| tree
2016-09-02	Berk Hess	Merge branch release-5-1 into release-2016	commit \| commitdiff \| tree
2016-09-02	Berk Hess	Fix Parrinello-Rahman with nstpcouple>1	commit \| commitdiff \| tree
2016-08-30	Berk Hess	Make virial reproducible	commit \| commitdiff \| tree
2016-08-27	Berk Hess	Reduce rounding errors in SETTLE	commit \| commitdiff \| tree
2016-08-24	Berk Hess	Fix Ewald surface+3DC corrections	commit \| commitdiff \| tree
2016-08-24	Berk Hess	Merge branch release-5-1 into release-2016	commit \| commitdiff \| tree
2016-08-23	Berk Hess	Remove variable precision gro writing	commit \| commitdiff \| tree
2016-08-17	Berk Hess	Fixed opening of wall table files	commit \| commitdiff \| tree
2016-08-15	Berk Hess	Reduce FE pair-list memory usage	commit \| commitdiff \| tree
2016-08-10	Berk Hess	Fix deadlock with thread-MPI	commit \| commitdiff \| tree
2016-08-09	Berk Hess	Fix twin-cutoff for GPU LJ pot-switch	commit \| commitdiff \| tree
2016-07-07	Berk Hess	Relax pull PBC check	commit \| commitdiff \| tree
2016-07-05	Berk Hess	Add checks for too much memory in g_nmeig	commit \| commitdiff \| tree
2016-07-03	Berk Hess	Add grompp check for pull group	commit \| commitdiff \| tree
2016-06-28	Berk Hess	Properly reset CUDA application clocks	commit \| commitdiff \| tree
2016-06-27	Berk Hess	Use sysconf(_SC_NPROCESSORS_ONLN)	commit \| commitdiff \| tree
2016-06-26	Berk Hess	Fix vsite bug with MPI+OpenMP	commit \| commitdiff \| tree
2016-06-24	Berk Hess	Fix Verlet buffer calculation with nstlist=1	commit \| commitdiff \| tree
2016-06-23	Berk Hess	More accurate GPU list splitting	commit \| commitdiff \| tree
2016-06-22	Berk Hess	Updated OpenCLTODOList.txt	commit \| commitdiff \| tree
2016-06-22	Berk Hess	Add nbnxn pair-list rebalancing	commit \| commitdiff \| tree
2016-06-22	Berk Hess	Remove OpenMP overhead at high parallelization	commit \| commitdiff \| tree
2016-06-22	Berk Hess	Correct GPU pair estimate for list splitting	commit \| commitdiff \| tree
2016-06-21	Berk Hess	Fix bug with fbposres+MPI+OpenMP	commit \| commitdiff \| tree
2016-06-20	Berk Hess	Increased tpx_incompatible_version to 30	commit \| commitdiff \| tree
2016-06-19	Berk Hess	Remove warnings on checkpoint mismatch	commit \| commitdiff \| tree
2016-06-17	Berk Hess	Remove std::thread::hardware_concurrency()	commit \| commitdiff \| tree
2016-06-14	Berk Hess	Fix OpenCL error with empty domains	commit \| commitdiff \| tree
2016-06-13	Berk Hess	Handle constraint errors with EM	commit \| commitdiff \| tree
2016-06-07	Berk Hess	Fix data race in hwinfo with thread-MPI	commit \| commitdiff \| tree
2016-06-03	Berk Hess	Handle partially frozen and constrained atoms	commit \| commitdiff \| tree
2016-05-31	Berk Hess	Reposition nbnxn filler particles	commit \| commitdiff \| tree
2016-05-31	Berk Hess	Avoid numerical overflow with overlapping atoms	commit \| commitdiff \| tree
2016-05-31	Berk Hess	Add check for finite energies	commit \| commitdiff \| tree
2016-05-30	Berk Hess	Add grompp check for unbound atoms	commit \| commitdiff \| tree
2016-05-23	Berk Hess	Fix bug in v-rescale thermostat & replica exchange	commit \| commitdiff \| tree
2016-05-10	Berk Hess	Optimized the vsite threading	commit \| commitdiff \| tree
2016-05-10	Berk Hess	Fix CUDA shmem bug	commit \| commitdiff \| tree
2016-05-10	Berk Hess	Support cmap with QMMM	commit \| commitdiff \| tree
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