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2020-11-11	Berk Hess	Update gmx msd documentation	commit \| commitdiff \| tree
2020-11-10	Berk Hess	Fix dHdl and foreign energy clearing at checkpointing	commit \| commitdiff \| tree
2020-11-09	Berk Hess	Move implementation to cpp file	commit \| commitdiff \| tree
2020-11-05	Berk Hess	Disable MTS with SD integrator	commit \| commitdiff \| tree
2020-11-05	Berk Hess	Copy position restraint parameters with MTS	commit \| commitdiff \| tree
2020-10-28	Berk Hess	Correct AWH initial histogram size	commit \| commitdiff \| tree
2020-10-27	Berk Hess	Refactor MTS preprocessing and checking	commit \| commitdiff \| tree
2020-10-21	Berk Hess	Fix pull code bug with DD and atom sets	commit \| commitdiff \| tree
2020-10-09	Berk Hess	Add MTS support for pull and AWH	commit \| commitdiff \| tree
2020-10-05	Berk Hess	Remove incorrect cycle suppression	commit \| commitdiff \| tree
2020-10-01	Berk Hess	Move computeSlowForces into stepWork	commit \| commitdiff \| tree
2020-09-30	Berk Hess	Move computeSlowForces into stepWork	commit \| commitdiff \| tree
2020-09-28	Berk Hess	Fix dispersion correction table generation	commit \| commitdiff \| tree
2020-09-25	Berk Hess	Fix grompp group handling with frozen system	commit \| commitdiff \| tree
2020-09-18	Berk Hess	Remove cutoff_scheme from t_forcerec and interaction_const_t	commit \| commitdiff \| tree
2020-09-17	Berk Hess	Move bNonbonded flag from t_forcerec to SimulationWorkload	commit \| commitdiff \| tree
2020-09-16	Berk Hess	Remove unnecessary condition in DD force buffer resizing	commit \| commitdiff \| tree
2020-09-15	Berk Hess	Only extend Ewald table when necessary	commit \| commitdiff \| tree
2020-09-15	Berk Hess	Fix task assignment with multiruns	commit \| commitdiff \| tree
2020-09-13	Berk Hess	Decouple nsttcouple and nstpcouple from nstlist	commit \| commitdiff \| tree
2020-09-10	Berk Hess	Add angles to ListedForces selections	commit \| commitdiff \| tree
2020-09-10	Berk Hess	Fix memory corruption with strings in grompp	commit \| commitdiff \| tree
2020-09-02	Berk Hess	Move listed and wall forces out of do_force_lowlevel()	commit \| commitdiff \| tree
2020-09-02	Berk Hess	Enable splitting of listed interaction calculation	commit \| commitdiff \| tree
2020-08-28	Berk Hess	Add SIMD version of harmonic bonds	commit \| commitdiff \| tree
2020-08-27	Berk Hess	Add ForceBuffers class	commit \| commitdiff \| tree
2020-08-14	Berk Hess	Add SIMD bonded tests and improve SIMD angles()	commit \| commitdiff \| tree
2020-08-13	Berk Hess	Add new FEP perturbation check functions	commit \| commitdiff \| tree
2020-08-12	Berk Hess	Fix virtual site vsiten indexing bug	commit \| commitdiff \| tree
2020-08-07	Berk Hess	Add accumulation checks to ForeignLambdaTerms	commit \| commitdiff \| tree
2020-07-31	Berk Hess	Move foreign potential energy accumulation	commit \| commitdiff \| tree
2020-07-06	Berk Hess	Move foreign potential energy accumulation	commit \| commitdiff \| tree
2020-06-26	Berk Hess	Move dispersion correction call to do_force()	commit \| commitdiff \| tree
2020-06-24	Berk Hess	Add class ListedForces	commit \| commitdiff \| tree
2020-06-24	Berk Hess	Change grompp disres cost to linear	commit \| commitdiff \| tree
2020-06-23	Berk Hess	Add virtual site with one constructing atom	commit \| commitdiff \| tree
2020-06-22	Berk Hess	Fix tpxio function type update table	commit \| commitdiff \| tree
2020-06-22	Berk Hess	Move soft-core parameters to interaction_const_t	commit \| commitdiff \| tree
2020-06-18	Berk Hess	Convert t_forcetable to C++	commit \| commitdiff \| tree
2020-06-05	Berk Hess	Remove COM from SETTLE	commit \| commitdiff \| tree
2020-06-03	Berk Hess	Fix missing PBC in SHAKE	commit \| commitdiff \| tree
2020-06-03	Berk Hess	Turn SettleData into a class	commit \| commitdiff \| tree
2020-05-20	Berk Hess	Remove t_mdatoms from Nbnxm setAtomProperties()	commit \| commitdiff \| tree
2020-05-19	Berk Hess	Refactor print_missing_interactions()	commit \| commitdiff \| tree
2020-05-14	Berk Hess	Extract postProcessForceWithShiftForces()	commit \| commitdiff \| tree
2020-05-12	Berk Hess	Extract helper force buffers to a separate class	commit \| commitdiff \| tree
2020-05-12	Berk Hess	Refactor virtual site interface	commit \| commitdiff \| tree
2020-05-07	Berk Hess	Avoid warning during PME tuning	commit \| commitdiff \| tree
2020-04-06	Berk Hess	Move force buffer resizing to mdsetup	commit \| commitdiff \| tree
2020-03-20	Berk Hess	Rename class Grid to BiasGrid in AWH module	commit \| commitdiff \| tree
2020-03-19	Berk Hess	Simplify finish_update()	commit \| commitdiff \| tree
2020-03-19	Berk Hess	Remove at_start from t_graph	commit \| commitdiff \| tree
2020-03-18	Berk Hess	Remove use of graph in do_force()	commit \| commitdiff \| tree
2020-03-18	Berk Hess	Use WholeMoleculeTransform for orires and epsilon-surface	commit \| commitdiff \| tree
2020-03-18	Berk Hess	Add WholeMoleculeTransform class	commit \| commitdiff \| tree
2020-03-17	Berk Hess	Convert t_graph to C++	commit \| commitdiff \| tree
2020-03-17	Berk Hess	Disable Ewald dipole correction without DD	commit \| commitdiff \| tree
2020-03-13	Berk Hess	Add tests for Ewald surface terms	commit \| commitdiff \| tree
2020-03-11	Berk Hess	Add tests for graph	commit \| commitdiff \| tree
2020-03-10	Berk Hess	Fix type in range and add tests	commit \| commitdiff \| tree
2020-03-07	Berk Hess	Make shake work without graph	commit \| commitdiff \| tree
2020-03-05	Berk Hess	Add InteractionDefinitions	commit \| commitdiff \| tree
2020-03-02	Berk Hess	Fix center of mass motion removal with frozen atoms	commit \| commitdiff \| tree
2020-03-02	Berk Hess	Fix grompp unbound atom check	commit \| commitdiff \| tree
2020-03-02	Berk Hess	Fix nrdf with partial COMM removal	commit \| commitdiff \| tree
2020-03-02	Berk Hess	Fix too small pairlist buffer on Intel GPUs	commit \| commitdiff \| tree
2020-02-21	Berk Hess	Add fatal error when multisim runs sharing state have...	commit \| commitdiff \| tree
2020-02-15	Berk Hess	Remove 1 pulse DD request	commit \| commitdiff \| tree
2020-02-05	Berk Hess	Actually fix PME forces with FE without perturbed q/LJ	commit \| commitdiff \| tree
2020-02-04	Berk Hess	Actually fix PME forces with FE without perturbed q/LJ	commit \| commitdiff \| tree
2020-01-23	Berk Hess	Fix DD rank count prime check	commit \| commitdiff \| tree
2020-01-22	Berk Hess	Minor cleanup in constraint and shellfc code	commit \| commitdiff \| tree
2020-01-22	Berk Hess	Fix illegal memory access in PME communication	commit \| commitdiff \| tree
2020-01-22	Berk Hess	Clarify COMM/posres grompp note	commit \| commitdiff \| tree
2020-01-20	Berk Hess	Use ArrayRef(WithPadding) in constraint code	commit \| commitdiff \| tree
2020-01-20	Berk Hess	Use std::vector in shellfc	commit \| commitdiff \| tree
2020-01-17	Berk Hess	Add check for shells and GPU update	commit \| commitdiff \| tree
2020-01-16	Berk Hess	Correct fixed redmine issue id from 3297 to 3296	commit \| commitdiff \| tree
2020-01-15	Berk Hess	Fix multisim with parallel simulation	commit \| commitdiff \| tree
2020-01-13	Berk Hess	Avoid unnecessary exclusion generation in DD	commit \| commitdiff \| tree
2019-12-22	Berk Hess	Use ListOfLists for atom to constraint mapping	commit \| commitdiff \| tree
2019-12-22	Berk Hess	Move nr_nonperturbed out of t_ilist	commit \| commitdiff \| tree
2019-12-19	Berk Hess	Expand ListOfLists pushBack() functionality	commit \| commitdiff \| tree
2019-12-19	Berk Hess	Remove exclusions from t_topology	commit \| commitdiff \| tree
2019-12-19	Berk Hess	Fix mdrun appending invalidating energy files	commit \| commitdiff \| tree
2019-12-18	Berk Hess	Change grompp decoupling SD warning to note	commit \| commitdiff \| tree
2019-12-17	Berk Hess	Add note for COM removal with position restraints	commit \| commitdiff \| tree
2019-12-16	Berk Hess	Use ListOfLists in gmx_mtop_t and gmx_localtop_t	commit \| commitdiff \| tree
2019-12-16	Berk Hess	Fix issues in ListOfLists	commit \| commitdiff \| tree
2019-12-12	Berk Hess	Add class ListOfLists	commit \| commitdiff \| tree
2019-12-02	Berk Hess	Add check for coupled constraints for CUDA update	commit \| commitdiff \| tree
2019-12-02	Berk Hess	Extract LINCS CUDA helper functions	commit \| commitdiff \| tree
2019-11-29	Berk Hess	Merge "Merge branch release-2019 into release-2020...	commit \| commitdiff \| tree
2019-11-28	Berk Hess	Update documenation for NPT GPU update	commit \| commitdiff \| tree
2019-11-28	Berk Hess	Remove assertion failure in AWH without initial stage	commit \| commitdiff \| tree
2019-11-28	Berk Hess	Fix bug with GPU pressure scaling at non T-scaling...	commit \| commitdiff \| tree
2019-11-26	Berk Hess	Fix issues with AWH with periodic pulling	commit \| commitdiff \| tree
2019-11-20	Berk Hess	Quiet pdb2gmx and use gmx_fatal	commit \| commitdiff \| tree
2019-11-19	Berk Hess	Fix bonded atom communication performance	commit \| commitdiff \| tree
2019-11-18	Berk Hess	Fix intermolecular interactions with DD	commit \| commitdiff \| tree
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