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2014-06-28	Mark Abraham	Use parallel terminology more consistently	commit \| commitdiff \| tree
2014-06-28	ngoga	Default SD integrator is now sd1 by Nicu Goga	commit \| commitdiff \| tree
2014-06-27	Erik Lindahl	Always set b-state posres, even if identical to a-state	commit \| commitdiff \| tree
2014-06-27	Erik Lindahl	Update g_density to handle bilayers better	commit \| commitdiff \| tree
2014-06-27	Erik Lindahl	Fix LJPME Lorentz-Berthelot combination rules	commit \| commitdiff \| tree
2014-06-27	Rossen Apostolov	Changed linking order to make Extrae work.	commit \| commitdiff \| tree
2014-06-27	Erik Lindahl	Improve PDB I/O (keep occupancy, b-factor, element)	commit \| commitdiff \| tree
2014-06-27	Carsten Kutzner	Remove obsolete pull-geometry option 'position' from...	commit \| commitdiff \| tree
2014-06-27	Roland Schulz	Fix Phi Platform file for MPI	commit \| commitdiff \| tree
2014-06-27	Erik Lindahl	Avoid warnings about coupling when free_energy=no	commit \| commitdiff \| tree
2014-06-27	Rossen Apostolov	Added information about dihedral restraints.	commit \| commitdiff \| tree
2014-06-27	Rossen Apostolov	Remove install_manifest.txt during make clean.	commit \| commitdiff \| tree
2014-06-26	Mark Abraham	Merge "Merge release-4-6 into release-5-0" into release-5-0	commit \| commitdiff \| tree
2014-06-25	Erik Lindahl	Updated Amber GBSA parameters	commit \| commitdiff \| tree
2014-06-25	Erik Lindahl	Make source compile under Linux X32 ABI	commit \| commitdiff \| tree
2014-06-25	Erik Lindahl	Make it harder for compiler to optimize away SIMD CMake...	commit \| commitdiff \| tree
2014-06-24	Mark Abraham	Manual fixes	commit \| commitdiff \| tree
2014-06-24	Magnus Lundborg	Improved check to decide if to add chain/residue.	commit \| commitdiff \| tree
2014-06-24	David van der Spoel	Added check in grompp for shells and inputrec issues.	commit \| commitdiff \| tree
2014-06-24	Erik Lindahl	Fixed GROMOS assignment of PRO-NH terminus torsions	commit \| commitdiff \| tree
2014-06-24	Erik Lindahl	Make sure duplicates bondeds are set from hackblocks	commit \| commitdiff \| tree
2014-06-24	Erik Lindahl	Clean up CMAP placement in parameter list	commit \| commitdiff \| tree
2014-06-24	Erik Lindahl	Added multisimulation info to log/output	commit \| commitdiff \| tree
2014-06-24	Rossen Apostolov	Extend version checking/warnings for checkpoint continuation	commit \| commitdiff \| tree
2014-06-23	Rossen Apostolov	Added tip5p to the list of watermodels in some FF.	commit \| commitdiff \| tree
2014-06-23	Erik Lindahl	Enable 4-letter resname in PDB output, keeps more pdbinfo.	commit \| commitdiff \| tree
2014-06-23	Erik Lindahl	Detect non-fatal warnings when trying CFlags for source	commit \| commitdiff \| tree
2014-06-23	Erik Lindahl	Enable xvgr output and labels for g_principal	commit \| commitdiff \| tree
2014-06-23	Erik Lindahl	Disallow extracting V/F from XTC files in g_traj	commit \| commitdiff \| tree
2014-06-23	Erik Lindahl	Warn if using nsteps=0 without continuation=yes	commit \| commitdiff \| tree
2014-06-21	Vedran Miletić	Use ${CMAKE_INSTALL_LIBDIR} as lib directory for tng_io...	commit \| commitdiff \| tree
2014-06-20	Berk Hess	Fix g_mindist with pbc=XY	commit \| commitdiff \| tree
2014-06-20	Rossen Apostolov	Fixed typo in oplsaa ASPH charges.	commit \| commitdiff \| tree
2014-06-20	Rossen Apostolov	Removed unused parameters and cleanup of inputrec.	commit \| commitdiff \| tree
2014-06-19	Roland Schulz	Fix ref error in constraint pull code	commit \| commitdiff \| tree
2014-06-19	Rossen Apostolov	Small typos in surface tension description.	commit \| commitdiff \| tree
2014-06-19	Magnus Lundborg	Bumped the TNG library to the latest version.	commit \| commitdiff \| tree
2014-06-18	Erik Lindahl	Fixed CMake 2.8.12+ CUDA dylib bugs and warnings on...	commit \| commitdiff \| tree
2014-06-18	Rossen Apostolov	Added reference to cmap in pdb2gmx.	commit \| commitdiff \| tree
2014-06-18	Berk Hess	Fixed sign error in posres dvdl	commit \| commitdiff \| tree
2014-06-18	Mark Abraham	Made mdrun warn when generic kernels are used	commit \| commitdiff \| tree
2014-06-17	Carlo Camilloni	Fix a Replica Exchange output problem	commit \| commitdiff \| tree
2014-06-17	Roland Schulz	Fix that skipping fails if target is 2nd frame	commit \| commitdiff \| tree
2014-06-17	Berk Hess	Removed rounding issue in nbnxn Ewald table	commit \| commitdiff \| tree
2014-06-14	Berk Hess	Fixed PME bug with #OpenMP-threads a large prime	commit \| commitdiff \| tree
2014-06-14	Rossen Apostolov	Added tip5pe water model to oplsa.	commit \| commitdiff \| tree
2014-06-14	Erik Lindahl	Make sure figure legends are adapted to xmgr/xmgrace	commit \| commitdiff \| tree
2014-06-13	Berk Hess	Changed appending file name error message	commit \| commitdiff \| tree
2014-06-13	David van der Spoel	Fix memory-usage error in g_chi	commit \| commitdiff \| tree
2014-06-13	Roland Schulz	Make nbnxn template and generated files match	commit \| commitdiff \| tree
2014-06-13	Erik Lindahl	Force g_bond to use structure file	commit \| commitdiff \| tree
2014-06-12	Erik Lindahl	Added dummy mass for charmm TYR aromatic vsites	commit \| commitdiff \| tree
2014-06-12	Berk Hess	Fixed perturbed wall interactions	commit \| commitdiff \| tree
2014-06-11	Berk Hess	Decoupled repl_ex_nst from nstcalcenergy	commit \| commitdiff \| tree
2014-06-11	Rossen Apostolov	Mapped HIS1 to HSD in charmm27.	commit \| commitdiff \| tree
2014-06-11	Erik Lindahl	Avoid writing xvgr formatting with -xvg none	commit \| commitdiff \| tree
2014-06-10	Erik Lindahl	Process negative sigma correctly with combrule 2 or 3	commit \| commitdiff \| tree
2014-06-09	Rossen Apostolov	Issue a warning for using gmx_rms -prev with large...	commit \| commitdiff \| tree
2014-06-09	Rossen Apostolov	Install libraries in correct directories on multiarch...	commit \| commitdiff \| tree
2014-06-09	Berk Hess	Set make_ndx max name length and count to 1024	commit \| commitdiff \| tree
2014-06-09	Erik Lindahl	Fixed the output format of g_principal	commit \| commitdiff \| tree
2014-06-09	Rossen Apostolov	Fixed typo in description of conversion factors.	commit \| commitdiff \| tree
2014-06-09	Erik Lindahl	Modify single/double EPS to agree with ISO C	commit \| commitdiff \| tree
2014-06-07	Erik Lindahl	Added package version to tng_io CMakelists.txt	commit \| commitdiff \| tree
2014-06-05	Berk Hess	Fix constraint virial with multiple time stepping	commit \| commitdiff \| tree
2014-06-05	Mark Abraham	New quotes	commit \| commitdiff \| tree
2014-06-04	Rossen Apostolov	Updated C-/N-terminal partial charges in Amber03.ff.	commit \| commitdiff \| tree
2014-06-03	Mark Abraham	Use RNG correctly for v-rescale thermostat	commit \| commitdiff \| tree
2014-06-01	Szilárd Páll	Add quote on the kT-kj/mol conversion factor	commit \| commitdiff \| tree
2014-06-01	Erik Lindahl	Fixed typo in manual	commit \| commitdiff \| tree
2014-05-31	David van der Spoel	Permit trjconv to read and write velocities with TNG...	commit \| commitdiff \| tree
2014-05-30	Mark Abraham	Finalize change from GMX_CPU_ACCELERATION to GMX_SIMD	commit \| commitdiff \| tree
2014-05-24	Rossen Apostolov	Simplified section "Porting".	commit \| commitdiff \| tree
2014-05-22	Rossen Apostolov	Normal modes don't work currently with virtual sites...	commit \| commitdiff \| tree
2014-05-22	Teemu Murtola	Fix static group list indices in selection prompt	commit \| commitdiff \| tree
2014-05-22	Berk Hess	Avoid energy drift with verlet-buffer-tolerance	commit \| commitdiff \| tree
2014-05-22	Mark Abraham	Add fatal errors for VV and twin-range MTS	commit \| commitdiff \| tree
2014-05-22	Mark Abraham	Clarified docs for use of mdrun -nstlist	commit \| commitdiff \| tree
2014-05-20	Justin Lemkul	Improvements to the g_lie help description.	commit \| commitdiff \| tree
2014-05-20	Rossen Apostolov	Added a note about using direction-periodic pulling.	commit \| commitdiff \| tree
2014-05-20	Rossen Apostolov	Added a note about unsupported Verlet cutoff + Buckingham.	commit \| commitdiff \| tree
2014-05-20	Mark Abraham	Add note about correct calling of wallcycle counter	commit \| commitdiff \| tree
2014-05-18	Mark Abraham	Fix indenting of .tpr parameter dump in mdrun log file	commit \| commitdiff \| tree
2014-05-09	Alexey Shvetsov	Fix clang 3.5 warnings regarding abs	commit \| commitdiff \| tree
2014-05-09	Berk Hess	Minor tweaks to the DD setup	commit \| commitdiff \| tree
2014-05-09	Roland Schulz	Fix comparison of array to NULL	commit \| commitdiff \| tree
2014-05-09	Roland Schulz	Merge "Merge branch release-4-6 into release-5-0" into...	commit \| commitdiff \| tree
2014-05-09	Roland Schulz	Fix OpenMP scope error	commit \| commitdiff \| tree
2014-04-29	Berk Hess	Removed truncation of nrdf in v-rescale thermostat	commit \| commitdiff \| tree
2014-04-24	Magnus Lundborg	More efficient TNG selection group creation	commit \| commitdiff \| tree
2014-04-23	Berk Hess	Fixed nbnxn FE list allocation issue	commit \| commitdiff \| tree
2014-04-21	Michael Shirts	Issue warnings for potential switch w/o defining switch...	commit \| commitdiff \| tree
2014-04-16	Magnus Lundborg	Fixed bug inverting compression precision.	commit \| commitdiff \| tree
2014-04-16	Mark Abraham	Fix and simplify version matching for running tests	commit \| commitdiff \| tree
2014-04-07	Mark Abraham	Fix invalid dereference in g_tune_pme	commit \| commitdiff \| tree
2014-04-07	Erik Lindahl	Make sure water optimization is disabled for esoteric...	commit \| commitdiff \| tree
2014-04-07	Teemu Murtola	Doxygen documentation for version.h	commit \| commitdiff \| tree
2014-04-03	Mark Abraham	Move string-parsing code to where it can be reused	commit \| commitdiff \| tree
2014-04-02	Roland Schulz	Add doc for spec. values of GMX_MAXBACKUP	commit \| commitdiff \| tree
2014-04-02	David van der Spoel	Removed possibility of compiling with GSL.	commit \| commitdiff \| tree
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