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2012-05-26	Mark Abraham	Continuing to fix threading on Cygwin	commit \| commitdiff \| tree
2012-04-19	Mark Abraham	Various improvements to shell code	commit \| commitdiff \| tree
2012-04-14	Mark Abraham	Described default output behaviour	commit \| commitdiff \| tree
2012-04-14	Mark Abraham	Clarified warning message	commit \| commitdiff \| tree
2012-04-14	Mark Abraham	Clarified warning string	commit \| commitdiff \| tree
2012-04-10	Mark Abraham	Made g_helix sensitive to CHARMM atom naming	commit \| commitdiff \| tree
2012-04-10	Mark Abraham	Permit threads build on Cygwin	commit \| commitdiff \| tree
2012-04-09	Mark Abraham	Documentation and error message enhancements	commit \| commitdiff \| tree
2012-04-09	Mark Abraham	Lots of manual updates	commit \| commitdiff \| tree
2012-04-09	Mark Abraham	Consolidated documentation of .mdp restraint options	commit \| commitdiff \| tree
2012-04-02	Mark Abraham	Improved pdb2gmx error message	commit \| commitdiff \| tree
2012-04-02	Mark Abraham	Keep CMake quiet about a Cygwin issue	commit \| commitdiff \| tree
2012-03-18	Mark Abraham	Warnings against equilibrating with P-R P-coupling	commit \| commitdiff \| tree
2012-03-15	Mark Abraham	Clarified wording of documentation	commit \| commitdiff \| tree
2012-03-14	Mark Abraham	Changed cryptic error messages about disk quota	commit \| commitdiff \| tree
2012-03-09	Mark Abraham	More editorial fixes to tool documentation	commit \| commitdiff \| tree
2012-03-09	Mark Abraham	Editorial changes to tools documentation	commit \| commitdiff \| tree
2012-03-08	Mark Abraham	Improved warning note with DD and periodic molecules	commit \| commitdiff \| tree
2012-03-08	Mark Abraham	Made description string for g_select -select clearer	commit \| commitdiff \| tree
2012-03-08	Mark Abraham	Improved cryptic error message	commit \| commitdiff \| tree
2012-02-24	Mark Abraham	Minor formatting fixes to .mdp option documentation	commit \| commitdiff \| tree
2012-02-23	Mark Abraham	Fix pdb2gmx -cmap in corner cases	commit \| commitdiff \| tree
2012-02-10	Mark Abraham	Fixed g_sham using more than three dimensions	commit \| commitdiff \| tree
2012-02-10	Mark Abraham	Integer multiplication that checks for overflow	commit \| commitdiff \| tree
2012-02-01	Mark Abraham	Fixed trjconv -sub	commit \| commitdiff \| tree
2012-02-01	Mark Abraham	Improved error message	commit \| commitdiff \| tree
2012-01-31	Mark Abraham	Made error message even more explicit	commit \| commitdiff \| tree
2012-01-31	Mark Abraham	Corrected use of ?: in conditional	commit \| commitdiff \| tree
2012-01-10	Mark Abraham	Fixed use of isfinite and _isfinite	commit \| commitdiff \| tree
2012-01-04	Mark Abraham	Added CMake Toolchain file for BlueGene/P	commit \| commitdiff \| tree
2011-12-29	Mark Abraham	Documented the function of g_cluster -cl -noav	commit \| commitdiff \| tree
2011-12-14	Mark Abraham	Re-fixed static linking of maths libraries under UNIX	commit \| commitdiff \| tree
2011-12-13	Mark Abraham	Relaxed some assumptions about trajectory times	commit \| commitdiff \| tree
2011-11-23	Mark Abraham	Fixed g_angle -f -or to copy times from -f to -or	commit \| commitdiff \| tree
2011-11-02	Mark Abraham	Fix for GB, double, SSE2 and optimized kernels	commit \| commitdiff \| tree
2011-11-01	Mark Abraham	Trigger correct kernels under Cygwin	commit \| commitdiff \| tree
2011-10-27	Mark Abraham	Made reading of binary matrices more robust	commit \| commitdiff \| tree
2011-10-19	Mark Abraham	Corrected charge of CHARMM zinc ion to +2	commit \| commitdiff \| tree
2011-10-06	Mark Abraham	Removed erroneous use of MASSV on BlueGene	commit \| commitdiff \| tree
2011-10-06	Mark Abraham	Fixes for GB kernel	commit \| commitdiff \| tree
2011-09-27	Mark Abraham	Added tip for converting .xpm to something useful	commit \| commitdiff \| tree
2011-09-26	Mark Abraham	Dropped some hints in the documentation	commit \| commitdiff \| tree
2011-09-26	Mark Abraham	Removed CMake warning for recent OpenMPI versions	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
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