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2010-09-07	Berk Hess	removed (nan) average printing with normal modes	commit \| commitdiff \| tree
2010-09-07	Berk Hess	fixed crash with parallel nm with cut-off's	commit \| commitdiff \| tree
2010-08-31	Berk Hess	avoided creation of neighborlists without j-particles	commit \| commitdiff \| tree
2010-08-26	Berk Hess	fixed bug that caused corrupted checkpoint files	commit \| commitdiff \| tree
2010-08-26	Berk Hess	pdb2gmx now only allows a mismatch of a sign (iso any...	commit \| commitdiff \| tree
2010-08-24	Berk Hess	fixed pdb2gmx using start name iso end name for C-terminus	commit \| commitdiff \| tree
2010-08-24	Berk Hess	fixed bug in search_rtp introduced in previous commit	commit \| commitdiff \| tree
2010-08-24	Berk Hess	updated gmx_membed.c for a VV update	commit \| commitdiff \| tree
2010-08-24	Berk Hess	fixed pdb2gmx behavior for nearly matching residue...	commit \| commitdiff \| tree
2010-08-23	Berk Hess	removed the pdb2gmx -cwd option and updated the pdb2gmx...	commit \| commitdiff \| tree
2010-08-23	Berk Hess	pdb2gmx now prints the force field dir before the selection...	commit \| commitdiff \| tree
2010-08-23	Berk Hess	fixed mpi hang/crash with separate pme nodes and dd...	commit \| commitdiff \| tree
2010-08-20	Berk Hess	added function do_cpte_n_reals to checkpoint.c	commit \| commitdiff \| tree
2010-08-20	Berk Hess	fixed automated DD/PME grid decomposition choice which...	commit \| commitdiff \| tree
2010-08-20	Berk Hess	disabled optimized IBM BlueGene converts2ints macro...	commit \| commitdiff \| tree
2010-08-20	Berk Hess	increased tpx_generation which should have been done...	commit \| commitdiff \| tree
2010-08-20	Berk Hess	eneconv now copies the new delta_t entry	commit \| commitdiff \| tree
2010-08-20	Berk Hess	added dt to energy file frames	commit \| commitdiff \| tree
2010-08-20	Berk Hess	added free and some comment to deprecated close_trj	commit \| commitdiff \| tree
2010-08-20	Berk Hess	fixed segv's in g_anaeig	commit \| commitdiff \| tree
2010-08-18	Berk Hess	reduced the warning limit for Berendsen T-coupling...	commit \| commitdiff \| tree
2010-08-18	Berk Hess	removed the bNEMD boolean from the main MD loop and...	commit \| commitdiff \| tree
2010-08-18	Berk Hess	added some comment to group grompp assignment options	commit \| commitdiff \| tree
2010-08-18	Berk Hess	added group comparison to gmxcheck and print groups...	commit \| commitdiff \| tree
2010-08-18	Berk Hess	fixed possible pathe string buffer overflow in get_libdir	commit \| commitdiff \| tree
2010-08-17	Berk Hess	added function rescale_velocities	commit \| commitdiff \| tree
2010-08-16	Berk Hess	gmx_rmpbc now guesses ePBC again for each frame	commit \| commitdiff \| tree
2010-08-16	Berk Hess	gmx_rmpbc gets natoms passed again, without natoms...	commit \| commitdiff \| tree
2010-08-16	Berk Hess	put omp pragma's in fft5d.c between ifdef's	commit \| commitdiff \| tree
2010-08-16	Berk Hess	added openmp pragma's for the fft5d transpose routines	commit \| commitdiff \| tree
2010-08-16	Berk Hess	fixed mdrun writes tpidist.xvg on all nodes	commit \| commitdiff \| tree
2010-08-16	Berk Hess	fixed segv in mdrun with replica exchange	commit \| commitdiff \| tree
2010-08-16	Berk Hess	fixed fatal error in mdrun file appending with -multi...	commit \| commitdiff \| tree
2010-08-13	Berk Hess	gmxcheck now prints rmsd's as %g iso %f	commit \| commitdiff \| tree
2010-08-13	Berk Hess	moved full precision real format definition to simple.h	commit \| commitdiff \| tree
2010-08-12	Berk Hess	reverted the last, non-cosmetic change to pme.c	commit \| commitdiff \| tree
2010-08-12	Berk Hess	minor cosmetic changes in pme.c	commit \| commitdiff \| tree
2010-08-12	Berk Hess	made the pdb2gmx occupancy warning more obvious	commit \| commitdiff \| tree
2010-08-12	Berk Hess	fixed incorrect pdb2gmx output with multiple (altloc...	commit \| commitdiff \| tree
2010-08-11	Berk Hess	removed -merge from the pdb2gmx manual and clarified...	commit \| commitdiff \| tree
2010-08-11	Berk Hess	fixed bug that caused a segv when snew failed	commit \| commitdiff \| tree
2010-08-10	Berk Hess	removed CYS2 from the Amber rtp files	commit \| commitdiff \| tree
2010-08-10	Berk Hess	removed pdb2gmx -cysh hidden option that should have...	commit \| commitdiff \| tree
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
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