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2010-02-22	Berk Hess	added slope print for g_energy -sum	commit \| commitdiff \| tree
2010-02-22	Berk Hess	corrected NH variables when reading old tpx and cpt...	commit \| commitdiff \| tree
2010-02-17	Berk Hess	some clean-up in the VV code in do_md and fixed the...	commit \| commitdiff \| tree
2010-02-17	Berk Hess	synchronized checkpointing and termination with mdrun...	commit \| commitdiff \| tree
2010-02-16	Berk Hess	fixed a typo in an error message	commit \| commitdiff \| tree
2010-02-16	Berk Hess	mdrun now also checks -npme with non-parallel compilation	commit \| commitdiff \| tree
2010-02-16	Berk Hess	added check for mdrun -dd and -npme without parallel...	commit \| commitdiff \| tree
2010-02-16	Berk Hess	fixed global signaling with VV	commit \| commitdiff \| tree
2010-02-15	Berk Hess	collected all the mdrun parallel signals into one data...	commit \| commitdiff \| tree
2010-02-15	Berk Hess	fixed deadlocks during checkpointing and termination	commit \| commitdiff \| tree
2010-02-15	Berk Hess	made mdrun npme guessing work more consistently	commit \| commitdiff \| tree
2010-02-15	Berk Hess	fixed output size estimates for energy and dhdl files	commit \| commitdiff \| tree
2010-02-15	Berk Hess	made read_xvg ignore a last non newline terminated...	commit \| commitdiff \| tree
2010-02-12	Berk Hess	fixed possible mdrun repetitive warning print with...	commit \| commitdiff \| tree
2010-02-12	Berk Hess	fixed temperature issue introduced in the last commit	commit \| commitdiff \| tree
2010-02-11	Berk Hess	made genion operate on the last solvent entry in top...	commit \| commitdiff \| tree
2010-02-10	Berk Hess	replaced the greek xvg symbol escape sequences in gmxlib...	commit \| commitdiff \| tree
2010-02-10	Berk Hess	made g_bar read the temperature for the dhdl.xvg files	commit \| commitdiff \| tree
2010-02-10	Berk Hess	changed -xvgr bool option to -xvg enum xmgrace/xmgr...	commit \| commitdiff \| tree
2010-02-09	Berk Hess	fixed incorrect virial when nstcalcenergy>0 and epc=no	commit \| commitdiff \| tree
2010-02-08	Berk Hess	changed g_energy -aver to print the average iso the sum	commit \| commitdiff \| tree
2010-02-08	Berk Hess	fixed drift in g_energy, broke a few commits ago	commit \| commitdiff \| tree
2010-02-08	Berk Hess	introduced STEPSTRSIZE for printing gmx_large_int_t	commit \| commitdiff \| tree
2010-02-08	Berk Hess	changed g_energy and g_bar error estimation to average...	commit \| commitdiff \| tree
2010-02-05	Berk Hess	cleaned up the g_energy energy storage and added error...	commit \| commitdiff \| tree
2010-02-04	Berk Hess	added unit for g_energy -sum	commit \| commitdiff \| tree
2010-02-04	Berk Hess	added missing include	commit \| commitdiff \| tree
2010-02-04	Berk Hess	made i/o error checking in gmxcpp stricter	commit \| commitdiff \| tree
2010-02-04	Berk Hess	fixed a memory leak in grompp cmap reading	commit \| commitdiff \| tree
2010-02-04	Berk Hess	removed commented out code in pdb2top	commit \| commitdiff \| tree
2010-02-04	Berk Hess	made VV bufstate reallocation cleaner	commit \| commitdiff \| tree
2010-02-03	Berk Hess	fgets2 now generates a fatal error when a line is longer...	commit \| commitdiff \| tree
2010-02-03	Berk Hess	made a fatal error message on the .vsd database more...	commit \| commitdiff \| tree
2010-02-03	Berk Hess	fixed bug in previous commit of pdb2top.c	commit \| commitdiff \| tree
2010-02-03	Berk Hess	Removed FF.dat	commit \| commitdiff \| tree
2010-02-03	Berk Hess	updated Gromos c-termini databases for pdb2gmx changes	commit \| commitdiff \| tree
2010-02-03	Berk Hess	fixed replace and add issues in pdb2gmx termini processing	commit \| commitdiff \| tree
2010-02-03	Berk Hess	renamed ga2la_home to ga2la_get_home, added ga2la_is_home	commit \| commitdiff \| tree
2010-02-02	Berk Hess	fixed incorrect water H type in gmx spc.itp spce.itp...	commit \| commitdiff \| tree
2010-02-02	Berk Hess	fixed bug in pdb2gmx tdb delete processing	commit \| commitdiff \| tree
2010-02-02	Berk Hess	fixed crash with vsites and PD	commit \| commitdiff \| tree
2010-02-01	Berk Hess	TER entries in pdb file now get translated into chain...	commit \| commitdiff \| tree
2010-02-01	Berk Hess	the c-termini databases can now retain OXT instead...	commit \| commitdiff \| tree
2010-02-01	Berk Hess	pdb2gmx can now rename and delete atoms form the input...	commit \| commitdiff \| tree
2010-01-29	Berk Hess	changed mdrun option -resethmaxh to -resethway and...	commit \| commitdiff \| tree
2010-01-29	Berk Hess	resolved incorrect symtab string free in pdb2gmx	commit \| commitdiff \| tree
2010-01-28	Berk Hess	implemented force field atom renaming files for pdb2gmx	commit \| commitdiff \| tree
2010-01-28	Berk Hess	added hidden option -resethmaxh to mdrun	commit \| commitdiff \| tree
2010-01-28	Berk Hess	pdb2gmx now checks for the existence of the water model...	commit \| commitdiff \| tree
2010-01-28	Berk Hess	renamed libfn function to gmxlibfn	commit \| commitdiff \| tree
2010-01-28	Berk Hess	pdb2gmx now writes the relative path to .top when the...	commit \| commitdiff \| tree
2010-01-28	Berk Hess	gmxcpp is now able to process #include dir/file where...	commit \| commitdiff \| tree
2010-01-28	Berk Hess	Made pdb2gmx print relative paths for ff files when...	commit \| commitdiff \| tree
2010-01-27	Berk Hess	fixed atomprop warning being issued natoms times	commit \| commitdiff \| tree
2010-01-27	Berk Hess	Removed two files in share/top accidentally revived...	commit \| commitdiff \| tree
2010-01-27	Berk Hess	Made ions.itp include ions.itp from the force field...	commit \| commitdiff \| tree
2010-01-27	Berk Hess	Moved all the ion model files to the force field subdirectories.	commit \| commitdiff \| tree
2010-01-27	Berk Hess	Moved all the water model files to the force field...	commit \| commitdiff \| tree
2010-01-27	Berk Hess	moved all force field files, except water and ion models...	commit \| commitdiff \| tree
2010-01-27	Berk Hess	pdb2gmx now detects and reads force field files from...	commit \| commitdiff \| tree
2010-01-27	Berk Hess	fixed two bugs introduced in the previous commit of...	commit \| commitdiff \| tree
2010-01-26	Berk Hess	fixed particle decomposition P-LINCS setup	commit \| commitdiff \| tree
2010-01-26	Berk Hess	renamed autocorr -fft option to -fttcorr	commit \| commitdiff \| tree
2010-01-26	Berk Hess	added pull_geometry=direction_periodic to mdp_opt.html	commit \| commitdiff \| tree
2010-01-26	Berk Hess	shortened too long names for GB bondeds	commit \| commitdiff \| tree
2010-01-26	Berk Hess	fixed some comments in forcerec.c	commit \| commitdiff \| tree
2010-01-26	Berk Hess	made mdrun -pforce also catch NAN forces	commit \| commitdiff \| tree
2010-01-26	Berk Hess	added missing nblist initializations	commit \| commitdiff \| tree
2010-01-25	Berk Hess	added missing cmap_grid copy in dd_init_local_top	commit \| commitdiff \| tree
2010-01-25	Berk Hess	fixed segv with integrator sd2	commit \| commitdiff \| tree
2010-01-25	Berk Hess	changed -v verbosity option to -verb to avoid confict...	commit \| commitdiff \| tree
2010-01-22	Berk Hess	added warning for using full electrostatics without...	commit \| commitdiff \| tree
2010-01-21	Berk Hess	made g_bar use a tolerance for lambda value comparison	commit \| commitdiff \| tree
2010-01-21	Berk Hess	corrected the description of gmx_within_tol	commit \| commitdiff \| tree
2010-01-19	Berk Hess	fixed residue renumbering for multi-residue molecules	commit \| commitdiff \| tree
2010-01-19	Berk Hess	added -group option to g_mindist	commit \| commitdiff \| tree
2010-01-19	Berk Hess	fixed incorrect residue renumbering in t_atoms read...	commit \| commitdiff \| tree
2010-01-18	Berk Hess	switched off automatic DD decomposition in z with ewald_geom=3dc	commit \| commitdiff \| tree
2010-01-18	Berk Hess	fixed incomplete (not incorrect) eneconv concatenation	commit \| commitdiff \| tree
2010-01-15	Berk Hess	implemented pdb2gmx residue renaming	commit \| commitdiff \| tree
2010-01-14	Berk Hess	removed superfluous dgdl from open_dhdl print	commit \| commitdiff \| tree
2010-01-14	Berk Hess	removed the cgnr option for replace in the termini...	commit \| commitdiff \| tree
2010-01-14	Berk Hess	cgnr is now properly read in ter db replace entries	commit \| commitdiff \| tree
2010-01-14	Berk Hess	fixed pdb2gmx -p dir/topol.top top include statements	commit \| commitdiff \| tree
2010-01-12	Berk Hess	fixed parallel mdrun termination and nstlist=-1	commit \| commitdiff \| tree
2010-01-12	Berk Hess	made checkpoiting work again in parallel	commit \| commitdiff \| tree
2010-01-11	Berk Hess	made molecules whole in confout after EM	commit \| commitdiff \| tree
2010-01-11	Berk Hess	made separate arrays for NH pressure variables	commit \| commitdiff \| tree
2010-01-11	Berk Hess	fixed compiler warning	commit \| commitdiff \| tree
2010-01-08	Berk Hess	fixed hang in compute_globals	commit \| commitdiff \| tree
2010-01-08	Berk Hess	made particle decompostion work again with lincs on...	commit \| commitdiff \| tree
2010-01-08	Berk Hess	made graph.edge a single array	commit \| commitdiff \| tree
2010-01-05	Berk Hess	add extra output file to g_bar	commit \| commitdiff \| tree
2010-01-05	Berk Hess	split md.c into md.c and runner.c	commit \| commitdiff \| tree
2010-01-05	Berk Hess	set nnhchains to 0 when not using NH	commit \| commitdiff \| tree
2010-01-05	Berk Hess	renamed restr. bond to restraint pot.	commit \| commitdiff \| tree
2010-01-04	Berk Hess	removed NH chains note when not using NH	commit \| commitdiff \| tree
2010-01-04	Berk Hess	implemented restraint bonds	commit \| commitdiff \| tree
2010-01-04	Berk Hess	fixed the sorting of 1-4 FE interactions for foreign...	commit \| commitdiff \| tree
2009-12-17	Berk Hess	fixed typos in the g_msd description	commit \| commitdiff \| tree
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