Gromacs

Versions 5.0.x

    Version as of 23:15, 17 Oct 2019

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    Release notes for 5.0-beta2

    • Fixed bug in forces for long-range correction for LJ-PME
    • Fixed memory leak writing xtc-groups, simplify and test XTC writing
    • Fixed checkpoint reading for essential dynamics data, #1392
    • Fixed non-working flat-bottom posres code.
    • Fixed precision in thermal expansion coefficient calc.
    • Fixed checkpointing with Google Native Client
    • Stopped printing quotes on gmx_fatal()
    • Made shell detection in GMXRC more robust #1213
    • Fixed Google Native Client build.
    • Changed use of compiler flags with GPU + C++11 #1390
    • Pass on the default value of radstep in make_edi -radfix is chosen without -ra\ dstep
    • Fixed aspects of essential dynamics
    • Fixed essential dynamics (ED) continuation from .cpt for reference=average
    • Fixed various compilation warning issues
    • Automated selection of rlist for Verlet-scheme NVE simulations
    • Implement "computational electrophysiology" simulations to maintain steady-sta\ te ionic concentration between the two comparments of a double-membrane system.
    • Added initial support for trajectories in the new TNG format. So the XTC forma\ t is no longer synonymous with the output of compressed positions. Further complet\ ion work is required.
    • Added nbnxn tree force reduction (intended to suit future Xeon Phi implementio\ n) #1420
    • Added SIMD support for Intel MIC
    • Added helpful note about changed default behaviour for cutoff-scheme #1414
    • Added requirement for 64-bit integer
    • Bumped GMX_BUILD_OWN_FFTW to version 3.3.3, corrected user messages, permitted\ supplying a local file URL, avoided problems with FFTW wanting a Fortran compiler\ by default
    • Updated libxml2 CMake detection
    • Added updates for checking that the system FFTW works correctly
    • Implemented new bash shell completion export. No support for other shells for \ now. #685 #1410.
    • Clarified OpenMP-related things in mdrun help/man
    • Various updates to documentation
    • Improved file name option help #969
    • Extended version information output
    • Fixed installation of HTML manual
    • Added quotes from the 2013 Nobel Prize addresses
    • Added ASPP and GLUP to residuetypes.dat to suit CHARMM force fields
    • Lots of refactoring and initial code modularization #1415
    • Removed hidden option gmx dump -xvg -f a.xtc (duplicates gmx traj -ox a.xtc)
    • Removed "gmx trjconv -app" that duplicates functionality present in gmx trjcat\
    • Renamed "gmx tpbconv" to "gmx convert-tpr"
    • Removed useless "trjcat -prec" option
    • Added lots of various kinds of tests
    • Cleaned up list of GROMACS authors
    • Removed RPM spec files, until someone wants to work out how to maintain them a\ utomatically.
    • Fixed installed headers
    • Reset SOVERSION for libgromacs #1147

    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 10:04, 29 Jan 2014 by mabraham