Gromacs

Versions 4.5.x

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    1. 1. Release notes for 4.5-beta3

    Version as of 16:29, 15 Sep 2019

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    Release notes for 4.5-beta3

    •       removed + from opls NA ion in ions.tip, overlooked in previous commit
    •       moved nstcalcenergy just before nstenergy in mdp, log and manual files
    •       added exclusion check for cg-cg innerloops
    •       env.var. GMX_NB_GENERIC no turns off solvent optimization as well
    •       corrected LJ on H of charmm tips3p
    •       made vrescale and Berendsen tcouple work with VV, although not perfect yet
    •       fixed PME communication range when first DD dim is not x
    •       added full precision option to g_traj and reformatted the source code
    •       grompp automatic nstcalcenergy setting now takes small nstenergy into acount
    •       fixed g_energy manual formatting issues
    •       gmxcheck now using the diagonal for relative tolerance of tensor elements and only compares terms with equal names, even when the number of terms differ
    •       removed commrec->nthreads from FAHCORE code
    •       gmxcheck now compares terms by name matching
    •       make_ndx now allows nearly all characters in atom and residue names, especially ' is useful for DNA and RNA
    •       sc_sigma now also sets the minimum value for the soft-core sigma, old tpr file will retain the old behavior
    •       fixed gmx_rmpbc undoing the shifting when x!=x_s
    •       readinp, used for e.g. mdp, no longer uses gmxcpp
    •       added -pbc option to g_traj
    •       corrected the (irrelevant) default ir->gb_dielectric_offset value when reading old tpr files
    •       made mdrun -seppot work with threads and -seppot now always append _node? to the log files
    •       removed pdb2gmx -cysh hidden option that should have been removed before
    •       removed CYS2 from the Amber rtp files
    •       fixed linking of inputrec.h
    •       make GMXRC.{bash,csh,zsh} export PKG_CONFIG_PATH
    •       Fixed documentation text according to bugzilla 486
    •       Fixed bug 487 according to provided patch.
    •       Fixed reuse of variable as temp variable before printing results.
    •       Fixed build issue for template program in double precision
    •       Modified TER record writing behaviour (only add after protein/DNA/RNA/polymers)
    •       Fixed accuracy issues in gmx_mm_log_ps(), and added lots of other transcendental functions in SSE.
    •       Added double precision SSE2 transcendental functions. Only Erf/Erfc missing now...
    •       Added out int-extraction macro to double precision SSE2 intrinsics header too.
    •       Fixed nonexistent return type on gmx_mm_sincos_pd
    •       Fixed a bug in index generation for non-adjacent protein chains
    •       Fixed incorrect #endif -> #else that caused the C all-vs-all GB to be called after the SSE one, which caused a segv.
    •       Copied CK-CB-N*-CT Amber improper to also list CK-CB-N*-CT (needed for DNA/RNA rtp files)
    •       Added NHE as an Amber aminoacid residue type
    •       Added NASM Cmake support
    •       cleanup: GMX_CG_INNERLOOP isn't used anymore
    •       Fixed configure.ac typo regrading qmmm-orca.
    •       Fix share/html/online/mdp_opt.html.
    •       Added missing NULL in chainsep enum in pdb2gmx.
    •       Fixed a typo in src/tools/CMakeLists.txt.
    •       Added an uninstall target to CMake builds.
    •       BAR calculations can now store energy histograms in .edr files.
    •       Now correctly checkpoints on dhdl histograms/lists that go to ener.edr.
    •       Small fix to deal with possible overflows in dh binning.
    •       minor addition to previus gcc 4.1.x disabling commit
    •       Fixes for PME-User-Switch.
    •       More PME-User-Switch fixes.
    •       Fixed compiler warnings in qm_orca.c.
    •       Fixed a segfault in selection code.
    Page last modified 19:20, 10 Aug 2010 by rossen