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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	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
2016-05-08	Berk Hess	Update mdrun termination info	commit \| commitdiff \| tree
2016-05-06	Berk Hess	OpenMP parallelization for pull	commit \| commitdiff \| tree
2016-04-20	Berk Hess	Fix pull legend with external potential	commit \| commitdiff \| tree
2016-04-19	Berk Hess	Allow rcoulomb>rvdw with PME	commit \| commitdiff \| tree
2016-04-19	Berk Hess	Broadcast pull external potential provider string	commit \| commitdiff \| tree
2016-04-19	Berk Hess	Fix gmx hbond group overlap check	commit \| commitdiff \| tree
2016-04-14	Berk Hess	Add QMMM checks	commit \| commitdiff \| tree
2016-04-03	Berk Hess	Correct nrdf for 1D/2D systems	commit \| commitdiff \| tree
2016-03-31	Berk Hess	Fix includes in readpull.cpp	commit \| commitdiff \| tree
2016-03-31	Berk Hess	Add option for external pull potential	commit \| commitdiff \| tree
2016-03-30	Berk Hess	Correct mdrun tMPI (non-)parallel error message	commit \| commitdiff \| tree
2016-03-26	Berk Hess	Add real/SIMD template for LJ-14 pairs	commit \| commitdiff \| tree
2016-03-22	Berk Hess	Avoid assertion failure in pme_loadbal_do	commit \| commitdiff \| tree
2016-03-22	Berk Hess	Make gmx vanhove work without PBC	commit \| commitdiff \| tree
2016-03-22	Berk Hess	LJ combination rule kernels for CUDA	commit \| commitdiff \| tree
2016-03-21	Berk Hess	Moved pull initialization back to mdrunner	commit \| commitdiff \| tree
2016-03-18	Berk Hess	Fix non-normalization of FFT autocorr	commit \| commitdiff \| tree
2016-03-14	Berk Hess	Remove restriction on dihdraltypes order	commit \| commitdiff \| tree
2016-03-12	Berk Hess	Split off Fermi kernel from CUDA kernel	commit \| commitdiff \| tree
2016-03-09	Berk Hess	Fix Ewald 3DC dipole with Verlet scheme	commit \| commitdiff \| tree
2016-03-04	Berk Hess	Converted csettle() to use real/SimdReal template	commit \| commitdiff \| tree
2016-03-03	Berk Hess	Use SIMD transpose scatter in bondeds	commit \| commitdiff \| tree
2016-03-03	Berk Hess	Use rvec4 for listed force buffer	commit \| commitdiff \| tree
2016-02-27	Berk Hess	Remove epsfac from GPU kernel inner-loops	commit \| commitdiff \| tree
2016-02-27	Berk Hess	Minor code reordering in GPU kernels	commit \| commitdiff \| tree
2016-02-26	Berk Hess	Fix compilation with Simd4Float, without Simd4Double	commit \| commitdiff \| tree
2016-02-19	Berk Hess	Fix excessive list splitting	commit \| commitdiff \| tree
2016-02-17	Berk Hess	Renamed nbnxn static const ints	commit \| commitdiff \| tree
2016-02-11	Berk Hess	Add SIMD version of pbc_dx_aiuc	commit \| commitdiff \| tree
2016-02-09	Berk Hess	Replaced nbnxn search+grid simd macros	commit \| commitdiff \| tree
2016-02-07	Berk Hess	Fix incorrect cmap parsing	commit \| commitdiff \| tree
2016-02-05	Berk Hess	Fix incorrect cmap parsing	commit \| commitdiff \| tree
2016-02-03	Berk Hess	Replaced literals in nbnxn lists by ints	commit \| commitdiff \| tree
2016-02-03	Berk Hess	Fix mdrun removing Verlet buffer with EM	commit \| commitdiff \| tree
2016-02-03	Berk Hess	Fix SETTLE error handling	commit \| commitdiff \| tree
2016-01-29	Berk Hess	Added documentation for pme grid indexing	commit \| commitdiff \| tree
2016-01-29	Berk Hess	Fix TPI ignoring PME mesh contributions.	commit \| commitdiff \| tree
2016-01-29	Berk Hess	Update -ntomp_pme -npme check	commit \| commitdiff \| tree
2016-01-29	Berk Hess	Add check for double perturbation	commit \| commitdiff \| tree
2016-01-29	Berk Hess	Fix LINCS triangle constraint thread issue	commit \| commitdiff \| tree
2016-01-28	Berk Hess	Update pair-list buffer manual	commit \| commitdiff \| tree
2016-01-24	Berk Hess	Fix exact continuation from non-energy steps	commit \| commitdiff \| tree
2016-01-24	Berk Hess	Fix energy file continuation with md-vv	commit \| commitdiff \| tree
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