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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
2010-06-03	Berk Hess	fixed bug in enum parsing error message	commit \| commitdiff \| tree
2010-06-03	Berk Hess	added VV parameters to mdp_opt.html	commit \| commitdiff \| tree
2010-06-02	Berk Hess	fixed more Gromos atom type name cases	commit \| commitdiff \| tree
2010-06-01	Berk Hess	cleaner fix for atom type case issue with GB parameters	commit \| commitdiff \| tree
2010-06-01	Berk Hess	fixed atom type case issue with GB parameters	commit \| commitdiff \| tree
2010-06-01	Berk Hess	fixed two GB bugs	commit \| commitdiff \| tree
2010-05-19	Berk Hess	fixed mdrun unwantingly modifying nstenergy and nstlog	commit \| commitdiff \| tree
2010-05-18	Berk Hess	implement SSE exp calculation for solve_pme	commit \| commitdiff \| tree
2010-05-17	Berk Hess	fixed some genborn include file details	commit \| commitdiff \| tree
2010-05-17	Berk Hess	reordered pme_solve_yzx arguments	commit \| commitdiff \| tree
2010-05-14	Berk Hess	minor pme_solve virial optimization	commit \| commitdiff \| tree
2010-05-14	Berk Hess	fixed segv with mdrun -npme 1	commit \| commitdiff \| tree
2010-05-12	Berk Hess	fixed case of atom types in the Gromos force fields	commit \| commitdiff \| tree
2010-05-12	Berk Hess	corrected pdb2gmx force field comments	commit \| commitdiff \| tree
2010-05-11	Berk Hess	made atom types case sensitive	commit \| commitdiff \| tree
2010-05-11	Berk Hess	fixed bug in pdb2gmx hdb initialization	commit \| commitdiff \| tree
2010-05-11	Berk Hess	added proper DNA and RNA residue recognition	commit \| commitdiff \| tree
2010-05-11	Berk Hess	added proper DNA and RNA residue recognition	commit \| commitdiff \| tree
2010-05-11	Berk Hess	fixed incorrect pdb2gmx residue name matching with...	commit \| commitdiff \| tree
2010-05-11	Berk Hess	fixed bug with pdb2gmx and multiple rtp files	commit \| commitdiff \| tree
2010-05-11	Berk Hess	added check for sys/time.h existence	commit \| commitdiff \| tree
2010-05-11	Berk Hess	updated and fine-tuned the coefficients for the PME...	commit \| commitdiff \| tree
2010-05-10	Berk Hess	removed include of complex.h in fft5d.h	commit \| commitdiff \| tree
2010-05-10	Berk Hess	fixed underallocation in gmx_fft_init_many_1d_real	commit \| commitdiff \| tree
2010-05-10	Berk Hess	fixed name in gromos43a1.ff Makefile.am	commit \| commitdiff \| tree
2010-05-10	Berk Hess	moved alcohol files from top to the force field subdirectories	commit \| commitdiff \| tree
2010-05-10	Berk Hess	moved alcohol files from top to the force field subdirectories	commit \| commitdiff \| tree
2010-05-10	Berk Hess	completion of the pdb2gmx residue renaming change	commit \| commitdiff \| tree
2010-05-07	Berk Hess	changed internal Gromacs naming of cys, his and lys	commit \| commitdiff \| tree
2010-05-07	Berk Hess	added a column for single residue chain to r2b file	commit \| commitdiff \| tree
2010-05-07	Berk Hess	fixed segv in grompp when gmxcpp reports an error	commit \| commitdiff \| tree
2010-05-07	Berk Hess	made grompp charge warning less sensitive to rounding...	commit \| commitdiff \| tree
2010-05-07	Berk Hess	made PME energy and virial calculation optional	commit \| commitdiff \| tree
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