BioD PNPI Git Repos - alexxy/gromacs.git/search

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2021-09-02	Berk Hess	Minor clean-up and optimization in DD topology	commit \| commitdiff \| tree
2021-08-30	Berk Hess	Make orires work with DD particle reordering	commit \| commitdiff \| tree
2021-08-25	Berk Hess	Enable atom reordering in WholeMoleculeTransform	commit \| commitdiff \| tree
2021-08-18	Berk Hess	Fix mdrun -ddorder pp_pme	commit \| commitdiff \| tree
2021-08-16	Berk Hess	grompp no longer modifies nstcomm	commit \| commitdiff \| tree
2021-07-02	Berk Hess	Revert "GROMACS 2021.3 release"	commit \| commitdiff \| tree
2021-07-01	Berk Hess	GROMACS 2021.3 release	commit \| commitdiff \| tree
2021-06-30	Berk Hess	Port basic pull test to gtest framework	commit \| commitdiff \| tree
2021-06-18	Berk Hess	Speed up grompp LJ parameter generation	commit \| commitdiff \| tree
2021-06-03	Berk Hess	Minor pull code cleanup	commit \| commitdiff \| tree
2021-05-27	Berk Hess	Add AWH references	commit \| commitdiff \| tree
2021-05-24	Berk Hess	Fix incorrectly sized ga2la hash table	commit \| commitdiff \| tree
2021-05-07	Berk Hess	Make debug printing work with empty domains	commit \| commitdiff \| tree
2021-05-05	Berk Hess	Convert t_oriresdata to C++	commit \| commitdiff \| tree
2021-05-03	Berk Hess	Clean up DD bonded interaction assignment	commit \| commitdiff \| tree
2021-04-23	Berk Hess	Specialize jacobi() for 3 dimensions	commit \| commitdiff \| tree
2021-04-13	Berk Hess	Implement dynamic pair search for EM	commit \| commitdiff \| tree
2021-03-31	Berk Hess	Use EnumerationArray for pull isAngleType	commit \| commitdiff \| tree
2021-03-31	Berk Hess	Use using for ArrayRef and RVec in pull code	commit \| commitdiff \| tree
2021-03-30	Berk Hess	Move dynamic pull groups and pull nthreads	commit \| commitdiff \| tree
2021-03-30	Berk Hess	Add coordIndex to t_pull_coord	commit \| commitdiff \| tree
2021-03-25	Berk Hess	Localize variables in do_lbfgs()	commit \| commitdiff \| tree
2021-03-25	Berk Hess	Fix grompp position restraint reference check	commit \| commitdiff \| tree
2021-03-23	Berk Hess	Add comparison operator to BasicVector	commit \| commitdiff \| tree
2021-03-19	Berk Hess	Remove const cast in update code	commit \| commitdiff \| tree
2021-03-01	Berk Hess	Fix mass perturbation to dH/dlambda	commit \| commitdiff \| tree
2021-02-22	Berk Hess	Reduce use of gmx_domdec_t in domdec_topology.cpp	commit \| commitdiff \| tree
2021-02-19	Berk Hess	Clean up DD reverse topology options	commit \| commitdiff \| tree
2021-02-10	Berk Hess	Fix gmx_rmpbc_init with InteractionDefinitions	commit \| commitdiff \| tree
2021-01-25	Berk Hess	MTS release note	commit \| commitdiff \| tree
2021-01-19	Berk Hess	Change default MTS force group selection	commit \| commitdiff \| tree
2021-01-12	Berk Hess	Avoid NMR restraints calls for MTS levels > 0	commit \| commitdiff \| tree
2020-12-10	Berk Hess	A check for perturbed listed pairs beyond rlist	commit \| commitdiff \| tree
2020-11-26	Berk Hess	Fix pull fatal error message	commit \| commitdiff \| tree
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
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