Gromacs

Versions 4.5.x

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    1. 1. Release notes for 4.5-beta3

    Version as of 12:41, 16 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.

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