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2010-08-09	Berk Hess	made mdrun -seppot work with threads and -seppot now...	commit \| commitdiff \| tree
2010-08-06	Berk Hess	Merge branch 'release-4-5-patches' of git@git.gromacs...	commit \| commitdiff \| tree
2010-08-06	Berk Hess	corrected the (irrelevant) default ir->gb_dielectric_offset...	commit \| commitdiff \| tree
2010-08-05	Berk Hess	added -pbc option to g_traj	commit \| commitdiff \| tree
2010-08-05	Berk Hess	readinp, used for e.g. mdp, no longer uses gmxcpp	commit \| commitdiff \| tree
2010-08-05	Berk Hess	fixed gmx_rmpbc undoing the shifting when x!=x_s	commit \| commitdiff \| tree
2010-08-05	Berk Hess	sc_sigma now also sets the minimum value for the soft...	commit \| commitdiff \| tree
2010-08-05	Berk Hess	make_ndx now allows nearly all characters in atom and...	commit \| commitdiff \| tree
2010-08-05	Berk Hess	gmxcheck now compares terms by name matching	commit \| commitdiff \| tree
2010-08-04	Berk Hess	removed commrec->nthreads from FAHCORE code	commit \| commitdiff \| tree
2010-08-04	Berk Hess	gmxcheck now using the diagonal for relative tolerance...	commit \| commitdiff \| tree
2010-08-04	Berk Hess	fixed g_energy manual formatting issues	commit \| commitdiff \| tree
2010-08-04	Berk Hess	grompp automatic nstcalcenergy setting now takes small...	commit \| commitdiff \| tree
2010-08-04	Berk Hess	added full precision option to g_traj and reformatted...	commit \| commitdiff \| tree
2010-08-03	Berk Hess	fixed PME communication range when first DD dim is...	commit \| commitdiff \| tree
2010-08-03	Berk Hess	made vrescale and Berendsen tcouple work with VV, although...	commit \| commitdiff \| tree
2010-08-02	Berk Hess	corrected LJ on H of charmm tips3p	commit \| commitdiff \| tree
2010-07-29	Berk Hess	completed partial rename of CYN to CYS for Amber	commit \| commitdiff \| tree
2010-07-28	Berk Hess	corrected the Amber aminoacids.r2b files	commit \| commitdiff \| tree
2010-07-28	Berk Hess	renamed pme_maxshift0/1 to pme_maxshift_x/y	commit \| commitdiff \| tree
2010-07-28	Berk Hess	replaced the Charmm vsite parameters (which were OPLS...	commit \| commitdiff \| tree
2010-07-28	Berk Hess	corrected a vsite parameter in the amber ff's	commit \| commitdiff \| tree
2010-07-28	Berk Hess	corrected Cl atom name in amber ions.itp	commit \| commitdiff \| tree
2010-07-28	Berk Hess	amber ff atomtypes change: corrected masses, removed...	commit \| commitdiff \| tree
2010-07-28	Berk Hess	update of amber03 aminoacids.rtp, accidentally left...	commit \| commitdiff \| tree
2010-07-27	Berk Hess	corrected mistakes in amber03 gbsa.itp	commit \| commitdiff \| tree
2010-07-27	Berk Hess	fixed typo in Makefile	commit \| commitdiff \| tree
2010-07-27	Berk Hess	moved ff_dum.itp to the gmx and gromos ff directories	commit \| commitdiff \| tree
2010-07-27	Berk Hess	corrected the amber vsite parameters	commit \| commitdiff \| tree
2010-07-27	Berk Hess	added his to opls r2b file	commit \| commitdiff \| tree
2010-07-27	Berk Hess	made the ff file naming of amber and charmm consistent...	commit \| commitdiff \| tree
2010-07-27	Berk Hess	corrected the amber water model files	commit \| commitdiff \| tree
2010-07-27	Berk Hess	fixed PME decomposition check for inverse DD order	commit \| commitdiff \| tree
2010-07-26	Berk Hess	renamed amber LYP to LYS and changed names for water...	commit \| commitdiff \| tree
2010-07-26	Berk Hess	removed HOH from amber rna.hdb	commit \| commitdiff \| tree
2010-07-26	Berk Hess	added missing entries for amber rna.hdb	commit \| commitdiff \| tree
2010-07-26	Berk Hess	cleaned up Amber hdb's and added HO4	commit \| commitdiff \| tree
2010-07-26	Berk Hess	renamed atom types from amber99_? etc. to the original...	commit \| commitdiff \| tree
2010-07-26	Berk Hess	fixed PME communication range (no silent errors)	commit \| commitdiff \| tree
2010-07-26	Berk Hess	removed building block RT from the lists in share/top	commit \| commitdiff \| tree
2010-07-26	Berk Hess	added residue and atom renaming for AMBER dna and rna	commit \| commitdiff \| tree
2010-07-26	Berk Hess	added DNA and RNA to the pdb2gmx .arn format	commit \| commitdiff \| tree
2010-07-26	Berk Hess	renamed O to O2 in amber rna.rtp	commit \| commitdiff \| tree
2010-07-26	Berk Hess	added natoms_force_constr to t_forcerec	commit \| commitdiff \| tree
2010-07-26	Berk Hess	renamed O to O2 in amber dna.rtp	commit \| commitdiff \| tree
2010-07-23	Berk Hess	removed garbage from checkpoint.c	commit \| commitdiff \| tree
2010-07-23	Berk Hess	fixed (rare) incorrect residue numbers when using gmx_mtop_a...	commit \| commitdiff \| tree
2010-07-23	Berk Hess	added openmm wrapper RF parameter checks	commit \| commitdiff \| tree
2010-07-19	Berk Hess	minor update to the previos appending fix	commit \| commitdiff \| tree
2010-07-19	Berk Hess	fixed mdrun append check when requested output file...	commit \| commitdiff \| tree
2010-07-06	Berk Hess	added mdp parameter for FE dH tables	commit \| commitdiff \| tree
2010-07-05	Berk Hess	changed the default maximum number of backups from...	commit \| commitdiff \| tree
2010-07-05	Berk Hess	removed a lot of slow FFT grid sizes from calc_grid...	commit \| commitdiff \| tree
2010-06-28	Berk Hess	documented pull cosine weighting	commit \| commitdiff \| tree
2010-06-28	Berk Hess	renamed mdrun -cptnum to -cpnum	commit \| commitdiff \| tree
2010-06-28	Berk Hess	added mdrun -cptnum option to keep and number checkpoints	commit \| commitdiff \| tree
2010-06-28	Berk Hess	reverted accidential change of tabangles in grompp...	commit \| commitdiff \| tree
2010-06-28	Berk Hess	added include update.h to coupling.c	commit \| commitdiff \| tree
2010-06-28	Berk Hess	added back const to gmx_sort compare params for qsort...	commit \| commitdiff \| tree
2010-06-24	Berk Hess	removed obsolete fftgrid code and disabled PPPM with...	commit \| commitdiff \| tree
2010-06-24	Berk Hess	changed pdb2gmx water model atom count detection	commit \| commitdiff \| tree
2010-06-24	Berk Hess	implemented nsteps=-1 for mdrun continuation and tpbconv	commit \| commitdiff \| tree
2010-06-24	Berk Hess	fixed smalloc.h and smalloc.c definition inconsistencies	commit \| commitdiff \| tree
2010-06-24	Berk Hess	Merge branch 'master' of git@git.gromacs.org:gromacs	commit \| commitdiff \| tree
2010-06-23	Berk Hess	removed statusio.h	commit \| commitdiff \| tree
2010-06-23	Berk Hess	fixed gmx_eneconv compiler warnings	commit \| commitdiff \| tree
2010-06-23	Berk Hess	fixed eneconv -dt option temporarily not writing averages	commit \| commitdiff \| tree
2010-06-22	Berk Hess	corrected edr format issue introduced today	commit \| commitdiff \| tree
2010-06-21	Berk Hess	add gmx_qsort routine, since glibc qsort is not threadsafe...	commit \| commitdiff \| tree
2010-06-21	Berk Hess	fixed typo in fatal_error call	commit \| commitdiff \| tree
2010-06-18	Berk Hess	now mdrun does not write the trr file when it would...	commit \| commitdiff \| tree
2010-06-18	Berk Hess	added env var GMX_MAXBACKUP	commit \| commitdiff \| tree
2010-06-17	Berk Hess	fix for the previous mdrun -rerun commit	commit \| commitdiff \| tree
2010-06-17	Berk Hess	mdrun -rerun now reads the rerun traj only on the master...	commit \| commitdiff \| tree
2010-06-17	Berk Hess	minor update for previous replex bugfix	commit \| commitdiff \| tree
2010-06-17	Berk Hess	fixed mdrun -rerun giving NaN with dispcorr	commit \| commitdiff \| tree
2010-06-17	Berk Hess	added water model selection and list file to pdb2gmx	commit \| commitdiff \| tree
2010-06-17	Berk Hess	made a separate tips3p.itp file for CHARMM	commit \| commitdiff \| tree
2010-06-17	Berk Hess	Merge branch 'master' of git@git.gromacs.org:gromacs	commit \| commitdiff \| tree
2010-06-16	Berk Hess	added spce to charmm27	commit \| commitdiff \| tree
2010-06-16	Berk Hess	fixed MPI crash when nat_home=0 in DD	commit \| commitdiff \| tree
2010-06-16	Berk Hess	restored the old order of the mdrun option and removed...	commit \| commitdiff \| tree
2010-06-16	Berk Hess	replaced more gmx_fatal by collective calls in DD	commit \| commitdiff \| tree
2010-06-16	Berk Hess	fixed atom naming in encad c-termini	commit \| commitdiff \| tree
2010-06-16	Berk Hess	with nsteps=-1 mdrun now prints ns/day estimate	commit \| commitdiff \| tree
2010-06-16	Berk Hess	added nsteps=-1 option to mdp_opt.html	commit \| commitdiff \| tree
2010-06-16	Berk Hess	all energy minimizers now do 0 steps with nsteps=0...	commit \| commitdiff \| tree
2010-06-15	Berk Hess	fixed incorrect pdb2gmx CYS2 to CYS renaming which...	commit \| commitdiff \| tree
2010-06-15	Berk Hess	allvsall loops now trigger particle decomposition	commit \| commitdiff \| tree
2010-06-15	Berk Hess	fatal_error in the DD initialization now calls MPI_Finalize...	commit \| commitdiff \| tree
2010-06-14	Berk Hess	added -cwd option to pdb2gmx	commit \| commitdiff \| tree
2010-06-11	Berk Hess	fixed mdrun counter resetting issues	commit \| commitdiff \| tree
2010-06-11	Berk Hess	optimized the number of threads	commit \| commitdiff \| tree
2010-06-10	Berk Hess	made DD work properly with all non-periodic system...	commit \| commitdiff \| tree
2010-06-10	Berk Hess	added more explanation to idef.h	commit \| commitdiff \| tree
2010-06-10	Berk Hess	fixed uninitialized variable in do_md	commit \| commitdiff \| tree
2010-06-10	Berk Hess	fixed particle decomposition load print	commit \| commitdiff \| tree
2010-06-04	Berk Hess	fixed pdb2gmx messing up coordinates when deleting...	commit \| commitdiff \| tree
2010-06-03	Berk Hess	added notes on mdp disre parameters	commit \| commitdiff \| tree
2010-06-03	Berk Hess	distance restraint ensemble averaging is no longer...	commit \| commitdiff \| tree
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