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2009-12-17	Berk Hess	fixed typos in the g_msd description	commit \| commitdiff \| tree
2009-12-17	Berk Hess	Merge branch 'master' of git@git.gromacs.org:gromacs	commit \| commitdiff \| tree
2009-12-17	Berk Hess	corrected the g_msd description	commit \| commitdiff \| tree
2009-12-15	Berk Hess	fixed the cycle counter n for the PME subdivision	commit \| commitdiff \| tree
2009-12-15	Berk Hess	added PME subdivision to cycle counters	commit \| commitdiff \| tree
2009-12-15	Berk Hess	added PME subdivision to cycle counters	commit \| commitdiff \| tree
2009-12-09	Berk Hess	fixed g_rdf -s -xy hanging	commit \| commitdiff \| tree
2009-12-07	Berk Hess	added new include files to include/Makefile.am	commit \| commitdiff \| tree
2009-12-02	Berk Hess	fixed incorrect g_bar check for missing lambda values	commit \| commitdiff \| tree
2009-12-02	Berk Hess	fixed ga2la index for empty DD cells	commit \| commitdiff \| tree
2009-11-19	Berk Hess	Merge branch 'master' of git@git.gromacs.org:gromacs	commit \| commitdiff \| tree
2009-11-19	Berk Hess	fixed the g_rmsf -res option	commit \| commitdiff \| tree
2009-11-11	Berk Hess	fixed compiler warning	commit \| commitdiff \| tree
2009-11-11	Berk Hess	added exclusion support for cg-cg loops	commit \| commitdiff \| tree
2009-11-11	Berk Hess	added exclusion support for cg-cg loops	commit \| commitdiff \| tree
2009-11-10	Berk Hess	Merge branch 'master' of git@git.gromacs.org:gromacs	commit \| commitdiff \| tree
2009-11-10	Berk Hess	fixed g_anaeig incorrect masses for fitting when the...	commit \| commitdiff \| tree
2009-11-06	Berk Hess	added check for MPI support in init_multisystem	commit \| commitdiff \| tree
2009-10-20	Berk Hess	fixed constraint error dump files not being written...	commit \| commitdiff \| tree
2009-10-14	Berk Hess	made mdrun -seppot work again	commit \| commitdiff \| tree
2009-10-08	Berk Hess	fixed compiler warnings	commit \| commitdiff \| tree
2009-10-08	Berk Hess	fixed compiler warning	commit \| commitdiff \| tree
2009-10-08	Berk Hess	split force.c into forcerec.c and force.c and added...	commit \| commitdiff \| tree
2009-10-07	Berk Hess	fixed hang in MPI call when serial mdrun was called...	commit \| commitdiff \| tree
2009-10-07	Berk Hess	added -ref and -fitxy options to g_rotmat	commit \| commitdiff \| tree
2009-10-07	Berk Hess	added env.var. to remove charge groups	commit \| commitdiff \| tree
2009-10-07	Berk Hess	fixed missing energy group energies due to incorrect...	commit \| commitdiff \| tree
2009-10-02	Berk Hess	made file appending work again	commit \| commitdiff \| tree
2009-10-02	Berk Hess	made pull pbc image choice consistent for extreme displaceme...	commit \| commitdiff \| tree
2009-10-02	Berk Hess	added check for user table spacing	commit \| commitdiff \| tree
2009-10-01	Berk Hess	fixed pdb2gmx bug when all hydrogens in the N-terminus...	commit \| commitdiff \| tree
2009-10-01	Berk Hess	removed space in g_sgangle y-axis unit	commit \| commitdiff \| tree
2009-10-01	Berk Hess	corrected g_sgangle y-axis unit	commit \| commitdiff \| tree
2009-09-30	Berk Hess	fixed v-site pbc bug with charge groups consisting...	commit \| commitdiff \| tree
2009-09-30	Berk Hess	moved the initialization of the grid ns lists	commit \| commitdiff \| tree
2009-09-30	Berk Hess	fixed bug with twin-range ns when not starting a simulation...	commit \| commitdiff \| tree
2009-09-28	Berk Hess	added index group non-SOL, removed group Other	commit \| commitdiff \| tree
2009-09-25	Berk Hess	made g_rotmat work with less atoms in trx than in tps	commit \| commitdiff \| tree
2009-09-24	Berk Hess	fixed incorrect #ifdef which did not allow vaccuum...	commit \| commitdiff \| tree
2009-09-23	Berk Hess	made g_sas read tps instead of tpx	commit \| commitdiff \| tree
2009-09-23	Berk Hess	fixed another issue with mdrun -rerun with a tpr without...	commit \| commitdiff \| tree
2009-09-18	Berk Hess	fixed xdrd reserved word clash with fortran	commit \| commitdiff \| tree
2009-09-18	Berk Hess	Merge branch 'master' of git@git.gromacs.org:gromacs	commit \| commitdiff \| tree
2009-09-18	Berk Hess	added more options for free-energy molecule coupling	commit \| commitdiff \| tree
2009-09-18	Berk Hess	new features for the termini database: replace now...	commit \| commitdiff \| tree
2009-09-17	Berk Hess	added -rmsd option to gmxcheck	commit \| commitdiff \| tree
2009-09-17	Berk Hess	made double precision edr file detection more robust	commit \| commitdiff \| tree
2009-09-16	Berk Hess	fixed setting of bF boolean in trxframe	commit \| commitdiff \| tree
2009-09-15	Berk Hess	added pull geometry distance_periodic and reorganized...	commit \| commitdiff \| tree
2009-09-14	Berk Hess	added state_prev to mdrun help text	commit \| commitdiff \| tree
2009-09-14	Berk Hess	removed unnecessary restrictions on pme_order	commit \| commitdiff \| tree
2009-09-10	Berk Hess	changed pdb2gmx -nocmap option to -cmap	commit \| commitdiff \| tree
2009-09-09	Berk Hess	made the nodecomm setup smarter	commit \| commitdiff \| tree
2009-09-04	Berk Hess	fixed incorrect mindist output for last residue with...	commit \| commitdiff \| tree
2009-09-04	Berk Hess	fixed g_nmens not writing trajectories	commit \| commitdiff \| tree
2009-09-04	Berk Hess	fixed resnr increase of 1 in confout.gro	commit \| commitdiff \| tree
2009-09-04	Berk Hess	proper out of range check for sizeof(off_t)=4 and large...	commit \| commitdiff \| tree
2009-09-02	Berk Hess	made mdrun -multi work again	commit \| commitdiff \| tree
2009-08-31	Berk Hess	fixed memory overallocation in genborn.c	commit \| commitdiff \| tree
2009-08-28	Berk Hess	added tool g_rotmat	commit \| commitdiff \| tree
2009-08-28	Berk Hess	fixed index group bug which made it impossible to select...	commit \| commitdiff \| tree
2009-08-28	Berk Hess	fixed crash in domdec with minimization and removed...	commit \| commitdiff \| tree
2009-08-26	Berk Hess	added shifts to the GB neighbor lists	commit \| commitdiff \| tree
2009-08-26	Berk Hess	fixed the grompp check from GBSA parameters	commit \| commitdiff \| tree
2009-08-25	Berk Hess	added option -vel to tpbconv	commit \| commitdiff \| tree
2009-08-25	Berk Hess	fixed segv when reading a checkpoint file into a trx...	commit \| commitdiff \| tree
2009-08-25	Berk Hess	removed erronous contribution of electric fields to...	commit \| commitdiff \| tree
2009-08-24	Berk Hess	removed the comm-mode check with SD and BD	commit \| commitdiff \| tree
2009-08-10	Berk Hess	changed i/o of gmx_step_t for possible issues with...	commit \| commitdiff \| tree
2009-08-07	Berk Hess	added env.var. to turn off the COM pull virial contribution	commit \| commitdiff \| tree
2009-08-07	Berk Hess	corrected COM pull position reference to init+rate...	commit \| commitdiff \| tree
2009-08-07	Berk Hess	added check for too many parameters in LJ types sections	commit \| commitdiff \| tree
2009-08-06	Berk Hess	fixed problems in pdb2gmx with chain identifiers and...	commit \| commitdiff \| tree
2009-08-06	Berk Hess	added check for Berendsen tcoupl with REMD	commit \| commitdiff \| tree
2009-08-06	Berk Hess	removed dhdl_lr from forcerec, no longer needed with...	commit \| commitdiff \| tree
2009-08-05	Berk Hess	updated addconf for new tpx variables	commit \| commitdiff \| tree
2009-08-05	Berk Hess	fixed fatal error with pbc and triclinic boxes	commit \| commitdiff \| tree
2009-08-05	Berk Hess	added check for comm removal	commit \| commitdiff \| tree
2009-08-03	Berk Hess	changed the twin-range integrator to a symplectic Trotter...	commit \| commitdiff \| tree
2009-07-30	Berk Hess	fixed incorrect manual layout	commit \| commitdiff \| tree
2009-07-29	Berk Hess	changed nan's to zeros for error estimates of constant...	commit \| commitdiff \| tree
2009-07-28	Berk Hess	fixed incorrect dHdl output for bondeds, introduced...	commit \| commitdiff \| tree
2009-07-27	Berk Hess	fixed rlistlong from do_int to do_real, introduced...	commit \| commitdiff \| tree
2009-07-15	Berk Hess	updated the energy file format to store averages over...	commit \| commitdiff \| tree
2009-07-15	Berk Hess	removed some load communication with -gcom	commit \| commitdiff \| tree
2009-07-14	Berk Hess	added mdp parameters nstcalcenergy and rlistlong and...	commit \| commitdiff \| tree
2009-07-13	Berk Hess	fixed segv in pdb2gmx with multiple (water)chains	commit \| commitdiff \| tree
2009-06-26	Berk Hess	moved the force wallcycle_stop from do_forcelowlevel...	commit \| commitdiff \| tree
2009-06-26	Berk Hess	fixed incorrect connelly surface with pbc	commit \| commitdiff \| tree
2009-06-26	Berk Hess	fixed segv in PME with mpirun -np 1	commit \| commitdiff \| tree
2009-06-26	Berk Hess	fixed segv in PME with mpirun -np 1	commit \| commitdiff \| tree
2009-06-26	Berk Hess	removed MPI calls when gmx_parallel_env=0	commit \| commitdiff \| tree
2009-06-25	Berk Hess	fixed missing communication of new reppow	commit \| commitdiff \| tree
2009-06-24	Berk Hess	fixed nrdf for T-coupling being incorrect for more...	commit \| commitdiff \| tree
2009-06-24	Berk Hess	changed g_traj summations from real to double	commit \| commitdiff \| tree
2009-06-24	Berk Hess	fixed the comm. bound cycle count when not doing DLB...	commit \| commitdiff \| tree
2009-06-22	Berk Hess	fixed the division by zero checks	commit \| commitdiff \| tree
2009-06-22	Berk Hess	added the repulsion power to the tpr file and added...	commit \| commitdiff \| tree
2009-06-22	Berk Hess	fixed gmx_within_tol being incorrect for comparing...	commit \| commitdiff \| tree
2009-06-22	Berk Hess	removed memory allocation and print for (non existing...	commit \| commitdiff \| tree
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