Gromacs

Versions 5.0.x

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    1. 1. Release notes for 5.0-beta1

    Version as of 05:07, 19 Oct 2019

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    Release notes for 5.0-beta1

    • Removed legacy CUDA non-bonded kernels #1382.
    • Removed restriction of one reference pull group #1346.
    • Made Verlet cutoff-scheme=Verlet the default. A few remaining unsupported cases.
    • Renamed verlet-buffer-drift to verlet-buffer-tolerance. Old mdp files are still processed correctly.
    • Let mdrun tune nstlist with CPU-only runs.
    • Added mdrun option -nstlist to set nstlist manually.
    • Added code for first stage of calculating LJ-interactions using Particle mesh Ewald.
    • Removed mdrun -ionize feature #1292.
    • Removed General Coupling Theory code #1292.
    • Removed forcefield-scan feature #1292.
    • Removed OpenMM code.
    • Made many changes to handling and form of documentation #685 #1242.
    • Moved manual repository into code repository.
    • Fixed manual for sc-coul description. #1331.
    • Updated bundled gmock to 1.7.0.
    • Added many new quotes .
    • Removed GMX_DOUBLE and unused #defines from config.h.
    • Installed fewer GROMACS header files. In particular, not those that are internal file-handling implementation details.
    • Fixed many problems with redundant, missing and transitive #include statements. Many remain.
    • Fixed many warnings that used to be suppressed, and removed the suppressions.
    • Removed lots of unused/duplicated/outdated/broken code, headers, documentation, variables, macros...
    • Added license for Sun XDR routines #1241.
    • Bumped CMake requirement to 2.8.8. Permits use of CMake "object libraries," and CMake-based detection of compiler ID and version. Avoids bug in add_library(GLOBAL).
    • Removed obsolete bundled CMake modules.
    • Made many minor rearrangements to CMake build system.
    • Added enumeration of valid build types for CMake GUI.
    • Added CMake helper for tracking cache variable changes.
    • Added CMake helper for dependent cache variables.
    • Added CMake helper for multichoice options.
    • Reorganized static/shared library CMake management.
    • Added CMake option to build a standalone mdrun binary only #685.
    • Re-implemented initialization routines to support invoking GROMACS binaries via "gmx toolname".
    • Documented how to add C++ tools using new framework.
    • Moved ngmx to C++, renamed it to view. Part of #673.
    • Added support for parallelized analysis data modules #869.
    • Made gmx-gangle more flexible with multiple angles.
    • Improved diagnostics with empty selections.
    • Updated g_cluster Rewrote the monte-carlo algorithm to do something useful, namely generate a smooth trajectory through all the frames where the ends of the trajectory are at maximum RMSD from each other.
    • Various clean-up and improvements in C++ tools. - Make gmx-select accept multiple selections for all output options. - Make gmx-gangle and gmx-distance accept dynamic selections. - Remove -dump option from gmx-select and remove commented code related to the same in the other tools. Part of #665.
    • Added statistics for gmx-distance.
    • Added lifetime statistics into gmx-select.
    • Replaced g_bond and g_dist #665.
    • Added new analysis tool to compute the free volume and total volume.
    • Added histogram output for 'gmx gangle'.
    • Added tool gmx sans.
    • Added pdbname selection keyword.
    • Allowed 'atomname' and 'atomtype' in selections.
    • Added flat-bottomed position restraints.
    • Extended g_wham to allow the selection of the pull groups to be applied in WHAM Also did a lot of minor cleanup and documentation to move to C++.
    • g_wham: fixed pullx.xvg reading issue with pull_geometry=cylinder.
    Page last modified 05:15, 5 Dec 2013 by mabraham