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2011-09-23	Mark Abraham	Minor house-keeping	commit \| commitdiff \| tree
2011-09-15	Mark Abraham	Fix trjconv -sub	commit \| commitdiff \| tree
2011-09-15	Mark Abraham	Warning about trjconv -sub needing many files open	commit \| commitdiff \| tree
2011-09-15	Mark Abraham	g_sham -mdata is an input file, not output file	commit \| commitdiff \| tree
2011-09-14	Mark Abraham	Format warning better	commit \| commitdiff \| tree
2011-09-13	Mark Abraham	Fix pdb2gmx -debug and .hdb files	commit \| commitdiff \| tree
2011-09-13	Mark Abraham	Fix for CMake finding LAPACK	commit \| commitdiff \| tree
2011-09-13	Mark Abraham	Added ACE and CT3 to CHARMM27 aminoacids.rtp	commit \| commitdiff \| tree
2011-09-13	Mark Abraham	Fixed charge groups of CHARMM27 DNA/RNA terminal H	commit \| commitdiff \| tree
2011-09-13	Mark Abraham	Fixes for CMake finding FORTRAN library names on POWER6	commit \| commitdiff \| tree
2011-09-06	Mark Abraham	Fix bug with large ints without MPI_IN_PLACE	commit \| commitdiff \| tree
2011-09-01	Mark Abraham	Made grompp note about non-zero charge more useful	commit \| commitdiff \| tree
2011-09-01	Mark Abraham	Re-implemented generating default protein index groups	commit \| commitdiff \| tree
2011-09-01	Mark Abraham	Adjusted construction of default index groups	commit \| commitdiff \| tree
2011-09-01	Mark Abraham	Fixed comment	commit \| commitdiff \| tree
2011-08-23	Mark Abraham	Fixed g_disre dereferencing cr	commit \| commitdiff \| tree
2011-08-23	Mark Abraham	Typo fix	commit \| commitdiff \| tree
2011-08-19	Mark Abraham	Explained terminal residues and AMBER in pdb2gmx -h	commit \| commitdiff \| tree
2011-08-16	Mark Abraham	Made free energy perturbation work with CMAP	commit \| commitdiff \| tree
2011-08-03	Mark Abraham	Fixed output bug in demux.pl	commit \| commitdiff \| tree
2011-07-17	Mark Abraham	Streamlined small part of pdb2gmx	commit \| commitdiff \| tree
2011-07-15	Mark Abraham	Reading a .g96 trajectory now causes fatal error	commit \| commitdiff \| tree
2011-07-11	Mark Abraham	Fix some identifier naming issues in last commit	commit \| commitdiff \| tree
2011-07-11	Mark Abraham	Avoided some integer overflows	commit \| commitdiff \| tree
2011-07-08	Mark Abraham	Clarified use of OPLS/AA zwitterion termini	commit \| commitdiff \| tree
2011-07-08	Mark Abraham	Fixed improper file close with GB and mdrun -debug	commit \| commitdiff \| tree
2011-07-08	Mark Abraham	Made pdb2gmx error message less cryptic	commit \| commitdiff \| tree
2011-06-29	Mark Abraham	Revert "draft"	commit \| commitdiff \| tree
2011-06-29	Mark Abraham	Improved error message and documentation	commit \| commitdiff \| tree
2011-06-29	Mark Abraham	draft	commit \| commitdiff \| tree
2011-06-21	Mark Abraham	Expanded LINCS warning text	commit \| commitdiff \| tree
2011-06-07	Mark Abraham	Fixed spelling of reproducible	commit \| commitdiff \| tree
2011-05-11	Mark Abraham	Added reference to g_sas -h	commit \| commitdiff \| tree
2011-05-11	Mark Abraham	Cleaned up g_sas help text	commit \| commitdiff \| tree
2011-05-09	Mark Abraham	Added hint about calling trjconv more than once	commit \| commitdiff \| tree
2011-05-09	Mark Abraham	Spaced out paragraphs in trjconv help	commit \| commitdiff \| tree
2011-05-02	Mark Abraham	Removed duplicate definition of md_print_warning()	commit \| commitdiff \| tree
2011-05-01	Mark Abraham	Fixed description of .mdp option to "h-bonds"	commit \| commitdiff \| tree
2011-04-14	Mark Abraham	Removed unnecessary #includes	commit \| commitdiff \| tree
2011-04-14	Mark Abraham	Deleted duplicated code	commit \| commitdiff \| tree
2011-04-14	Mark Abraham	Moved various support functions for do_md into mdlib	commit \| commitdiff \| tree
2011-04-14	Mark Abraham	Moved iterated-constraints code into mdlib	commit \| commitdiff \| tree
2011-04-14	Mark Abraham	Moved heuristic neighbor-list code into mdlib	commit \| commitdiff \| tree
2011-04-14	Mark Abraham	Fixed code duplication	commit \| commitdiff \| tree
2011-04-14	Mark Abraham	Fixed header #ifndef test	commit \| commitdiff \| tree
2011-03-30	Mark Abraham	Removed useless const qualifier	commit \| commitdiff \| tree
2011-03-30	Mark Abraham	Suppressed Cygwin C-only compiler warnings	commit \| commitdiff \| tree
2011-03-26	Mark Abraham	Fixed g_cluster logic error	commit \| commitdiff \| tree
2011-03-26	Mark Abraham	Made gmx_rmpbc_t object functions not segfault	commit \| commitdiff \| tree
2011-03-26	Mark Abraham	Fixed matio.c sfree() that made DvdS cry.	commit \| commitdiff \| tree
2011-03-08	Mark Abraham	Added grompp note about avoiding zero-step EM	commit \| commitdiff \| tree
2011-02-16	Mark Abraham	Clarified source of g_rmsf reference frame	commit \| commitdiff \| tree
2011-02-13	Mark Abraham	Added workaround for F_GB13 duplicates	commit \| commitdiff \| tree
2011-02-13	Mark Abraham	Fixed erroneous floating-point comparison	commit \| commitdiff \| tree
2011-02-12	Mark Abraham	Added note about doing repeat invocations of genbox	commit \| commitdiff \| tree
2011-02-11	Mark Abraham	Removed ancient CVS tag lines	commit \| commitdiff \| tree
2011-02-11	Mark Abraham	Used some spacing to make code readable	commit \| commitdiff \| tree
2011-02-11	Mark Abraham	Used symbolic constant more consistently	commit \| commitdiff \| tree
2011-02-11	Mark Abraham	Made the "multiple settles" fatal error more helpful	commit \| commitdiff \| tree
2011-02-02	Mark Abraham	Fixed minor issue with replica exchange	commit \| commitdiff \| tree
2011-01-28	Mark Abraham	Added forgotten file	commit \| commitdiff \| tree
2011-01-28	Mark Abraham	Turned g_options into a normal GROMACS tool	commit \| commitdiff \| tree
2011-01-28	Mark Abraham	Renamed src/tools/options.c	commit \| commitdiff \| tree
2011-01-28	Mark Abraham	Improved grompp documentation	commit \| commitdiff \| tree
2011-01-25	Mark Abraham	Improved genion -h	commit \| commitdiff \| tree
2011-01-25	Mark Abraham	Relocated some t_matrix documentation	commit \| commitdiff \| tree
2011-01-25	Mark Abraham	Improved do_dssp -ssdump output	commit \| commitdiff \| tree
2011-01-25	Mark Abraham	Improved do_dssp -sc output	commit \| commitdiff \| tree
2011-01-23	Mark Abraham	Remove g_highway from list of programs	commit \| commitdiff \| tree
2011-01-23	Mark Abraham	Improved conversion of documentation to LaTeX	commit \| commitdiff \| tree
2011-01-23	Mark Abraham	Improved consistency of text style usage	commit \| commitdiff \| tree
2011-01-23	Mark Abraham	Minor wording fixes	commit \| commitdiff \| tree
2011-01-23	Mark Abraham	Moved options.c to tools subdir	commit \| commitdiff \| tree
2011-01-23	Mark Abraham	cmake: added back gsl support (GMX_GSL, disabled by...	commit \| commitdiff \| tree
2011-01-20	Mark Abraham	Added NHE to OPLS/AA pdb2gmx hydrogen database	commit \| commitdiff \| tree
2011-01-20	Mark Abraham	Made gmxdump error message clearer.	commit \| commitdiff \| tree
2011-01-18	Mark Abraham	Improved .mdp file comment about the 'define' field	commit \| commitdiff \| tree
2011-01-17	Mark Abraham	Fix Angstrom <=> nm error in documentation	commit \| commitdiff \| tree
2011-01-13	Mark Abraham	Made src/kernel/repl_ex.c legible	commit \| commitdiff \| tree
2011-01-07	Mark Abraham	Added note that g_msd -mol does treat PBC (by making...	commit \| commitdiff \| tree
2011-01-07	Mark Abraham	Implemented effective test for MPI_IN_PLACE, thanks...	commit \| commitdiff \| tree
2011-01-06	Mark Abraham	Stop CMake defaulting to turning off compiler warnings...	commit \| commitdiff \| tree
2010-12-06	Mark Abraham	Added comments and workaround for IBM's BlueGene(/L...	commit \| commitdiff \| tree
2010-11-22	Mark Abraham	Added a hint to the documentation for creating .tpr...	commit \| commitdiff \| tree
2010-11-12	Mark Abraham	Minor trjconv documentation formatting fix	commit \| commitdiff \| tree
2010-11-12	Mark Abraham	g_densmap -od writes a .dat file and prevents writing...	commit \| commitdiff \| tree
2010-11-09	Mark Abraham	GMX_POWERPC_INVSQRT should be OFF in CMakeLists.txt...	commit \| commitdiff \| tree
2010-11-07	Mark Abraham	Made mdrun exit with a fatal error for EM or NM with...	commit \| commitdiff \| tree
2010-11-06	Mark Abraham	Fixed .xvg legends for g_sas options -or and -oa	commit \| commitdiff \| tree
2010-10-24	Mark Abraham	Don't sprintf variable-sized input into fixed-size...	commit \| commitdiff \| tree
2010-10-22	Mark Abraham	Re-enabled for BlueGene/L an optimization in the BG...	commit \| commitdiff \| tree
2010-10-22	Mark Abraham	Rearranged cmake+BlueGene solution to have the same...	commit \| commitdiff \| tree
2010-10-22	Mark Abraham	Made GMX_POWERPC_INVSQRT work properly on Power6 and...	commit \| commitdiff \| tree
2010-10-22	Mark Abraham	Power6 FORTRAN kernels do not work on PPC440 or PPC450...	commit \| commitdiff \| tree
2010-10-22	Mark Abraham	Fixing a trivial mangle introduced in b5d842ff1d94174b6e7012...	commit \| commitdiff \| tree
2010-10-20	Mark Abraham	Fixed cmake to work with BlueGene/L. This fix does...	commit \| commitdiff \| tree
2010-10-05	Mark Abraham	Fix manual references for 'continuation', rather than...	commit \| commitdiff \| tree
2010-10-05	Mark Abraham	mk_dlist() changed its parameter list, so its declaration...	commit \| commitdiff \| tree
2010-09-23	Mark Abraham	Fixes for g_chi for bugzilla 569, so that it now uses...	commit \| commitdiff \| tree
2010-09-23	Mark Abraham	Extensions to the gmx_residuetypes_t API to meet the...	commit \| commitdiff \| tree
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