Gromacs

Versions 5.0.x

    Version as of 05:05, 19 Oct 2019

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    Release notes for 5.0-rc1

    • Added full support in nbnxn kernels for perturbed non-bonded interactions in free-energy calculations
    • Added full support in nbnxn kernels for LJ force and potential switching, which are selected through vdw_modifier
    • Added full support in nbnxn kernels for LJ-PME
    • Fixed Verlet-scheme buffer estimate when rvdw-switch=0. Updated estimate formula in the manual and added a missing factor of 2 (the code did use the factor of 2).
    • Added new VDW kernel flavour for LJ-PME and updated group kernels. Group-scheme LJ-PME now calculates the same properties as Verlet-scheme. The previous group kernels implemented the non-bonded interactions as described in J. Chem. Theory Comput., 2013, 9 (8), pp 3527–3537. These are now updated to subtract the grid contribution in real space, which corrects for any difference in the reciprocal-space part from the use of approximate LJ parameters. Group kernels + LJ-PME now supports modifiers.
    • Added CUDA GPU LJ-PME nbnxn kernels (geometric as well as Lorentz-Berthelot (LB) combination rules)
    • Added CUDA GPU kernels for force and potential switching
    • Improved CUDA non-bonded kernel performance slightly
    • Bumped the required CUDA version to 4.0 #1382
    • CUDA cut-off kernels now shift exclusion energies This is to make the GPU kernels consistent with the CPU nbnxn kernels, which for eeltype=cut-off modifier=potential-shift effectively do reaction-field with epsilon_rf=1. Also implemented shifting of the Coulomb potential for the group cut-off scheme for non-excluded pairs only. The manual now explains these details. Also fixed the generic group kernel with an exact cutoff for either Coulomb or VdW.
    • Fixed bug leading to fatal failures when -gpu_id was not specified
    • Redesigned SIMD module to support all x86 SIMD (including Xeon Phi and AVX2), and BlueGene/Q, and added unit tests
    • Added AVX2 detection to cmake
    • Add cmake option for Reference SIMD type
    • Added message to warn that group kernels are deprecated
    • Replaced all mdrun random number generators with a cycle-based random number generator, to enhance reproducibility in parallel or after continuations. State no longer needs to be stored in the checkpoint file #995
    • Use pseudo-random instead of random streams to intialize seeds
    • Changed behaviour to use random seeds by default, rather than the same default seed, because a stocastic simulation not being reproducible by default is less surprising
    • Made ld-seed a 64-bit integer, so more than 4 billion sequences are potentially available
    • Added informational messages for leapfrog + MTTK to prevent silently producing wrong results. Added note about deprecation and planned removal of MTTK + constraints. #1292
    • Added combined angle-torsion potentials for use with Martini force field
    • Added Interactive Molecular Dynamics (IMD) to allow interaction with and monitoring of a running molecular dynamics simulation.
    • Finished support for Xeon Phi in native mode (when completed, offload mode will work better)
    • Added SIMD reduction in PME
    • Fixed seperate PME nodes without LJ-PME
    • Fixed aligned store to unaligned memory in PME
    • Minor improvements to ewald_LRcorrection for LJ-PME
    • Fixed free-energy perturbation with separate PME nodes
    • Fixed bug in LJ-PME when running with no electrostatic interactions
    • PME load balancing now works with LJ-PME
    • Added LJ-PME and LJ Potential-switch to PME load estimate
    • Bumped TNG to latest version.
    • Removed dependency on TNG in trxio.h #1452
    • Removed option to use OpenMP with the TNG library #1432
    • Enabled TNG on Windows builds by default
    • Added check that zlib can actually be linked when required for TNG #1435
    • Cleaned up .log file dump of inputrec New wide name made formatting ugly. Renamed a few things to follow .mdp convention.
    • Improved wallcycle reporting Removed reporting of MPI and thread counts on each row, in favour of a header with that information #1188
    • Fixed segfaults when comparing .tpr files from different generations if number of interaction types didn't match
    • Add enum and docs for using tpx_version
    • Fixed incorrect grid cell size in gmx sas -nopbc #1445
    • Converted gmx sas to the C++ framework, some minor changes in behaviour and user interface
    • Add support for non-uniform X axis in array data
    • Added safety check for fitting group in anaeig
    • Removed gmx kinetics (and support for linking to GSL). #1472
    • Added various improvements for keeping compilers happy and productive
    • Added Cray compiler support (SIMD, atomics, cycle counting, OpenMP)
    • Updated internal Boost to latest 1.55.0
    • Removed deprecated Encad FF
    • Added new amber99sb-ildn-bsc0 force field. It extends the original amber99sb-ildn with new parameters for nucleic acids, while the protein parameters are the same in both force fields.
    • Removed ions.itp from GMX/share/top directory
    • Removed the deprecated gmx and gmx2 force fields.
    • Removed support for .g87 and .xyz I/O formats
    • Removed particle decomposition #1292
    • Renamed ffopen and ffclose to gmx_ff* #1250
    • Fixed printing of integers with MSVC
    • Fixed mdrun crash when rdtscp is not supported by the CPU and exposed CMake variable GMX_USE_RDTSCP to control its use #1428
    • Fixed harmless bug with combination of group and twin-range
    • Fixed segfault with genbox and added integration tests for its major functionality #1393
    • Fixed several issues with using the vmd I/O libraries
    • Fixed and simplified use of rpath
    • Fixed issue with GMX_BUILD_OWN_FFTW where cmake was eating slashes
    • Fixed that expanded ensemble dhdl header should not specify a single lambda
    • Fixed issue with allocating 1MB on heap for MD5 sum while checkpointing on Windows
    • Updated stuff for old BlueGene - L and P are no longer supported
    • Removed Cygwin+MingW from installguide, neither are supported
    • Updated and improved Andersen thermostat documentation
    • Add fatal error for Andersen+constraints+domain decomposition
    • Clarified use of table-extension
    • Added documentation for using Doxygen
    • Added notes on portability aspects in install guide #1428
    • Cleaned up and documented options for domain decomposition
    • Added minor fix to permit warning-free use of Andersen thermostat
    • Split genbox into 'solvate' and 'insert-molecules', cleaning up, retaining all old working functionality and improving documentation
    • Made 'gmx -h' invariant wrt. provided options
    • Improved floating point comparisons in unit tests
    • Added integration tests for replica exchange
    • Added some overview docs for unit testing, wrapper binary implementation, and using Gromacs as a library
    • Added gmx_is_{single,double}_precision to allows easy detection by third-party code of the precision with which GROMACS was compiled
    • Fixed build of share/template when installed
    • Implemented new shell completion generation for command-line options #969 and #1410
    • Fixed shell completions of ffMULT options #1159, related to #1410, and other filename completions
    • Added new quotes
    • Added "release with asserts" build type, mostly for use in automated testing
    • Added ThreadSanitizer build type for helping detect misuse of thread operations
    • Fixed Reference Build
    • Added fixes to keep clang Address Sanitizer happy
    • Disabled shared libraries by default for the mdrun-only build
    • Added support for linking to profiler Extrae.

    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 -radstep
    • 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-state ionic concentration between the two comparments of a double-membrane system.
    • Added initial support for trajectories in the new TNG format. So the XTC format is no longer synonymous with the output of compressed positions. Further completion work is required.
    • Added nbnxn tree force reduction (intended to suit future Xeon Phi implemention) #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 automatically.
    • 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 15:13, 7 Apr 2014 by mabraham