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Versions 4.5.x

    Version as of 16:44, 22 Sep 2019

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    Release notes for 4.5-beta4

    •       fixed bug that caused a segv when snew failed
    •       removed -merge from the pdb2gmx manual and clarified the new -chainsep option
    •       fixed incorrect pdb2gmx output with multiple (altloc) atom entries in specbonds
    •       made the pdb2gmx occupancy warning more obvious
    •       gmxcheck now prints rmsd's as %g iso %f
    •       fixed fatal error in mdrun file appending with -multi or -seppot
    •       fixed segv in mdrun with replica exchange
    •       fixed mdrun writes tpidist.xvg on all nodes
    •       added openmp pragma's for the fft5d transpose routines
    •       gmx_rmpbc gets natoms passed again, without natoms many tool could not parse trajectories of a part of the system. And added gmx_rmpbc_trxfr
    •       gmx_rmpbc now guesses ePBC again for each frame
    •       added function rescale_velocities
    •       added group comparison to gmxcheck and print groups names in gmxdump
    •       added some comment to group grompp assignment options
    •       removed the bNEMD boolean from the main MD loop and stored it in gmx_ekindata_t
    •       reduced the warning limit for Berendsen T-coupling tau_t/dt to 5 steps
    •       fixed segv's in g_anaeig
    •       added dt to energy file frames
    •       eneconv now copies the new delta_t entry
    •       increased tpx_generation which should have been done in the previous commit of tpxio.c: 0c288518
    •       disabled optimized IBM BlueGene converts2ints macro because of bugzilla 429
    •       fixed automated DD/PME grid decomposition choice which excluded the optimum in certain cases
    •       added function do_cpte_n_reals to checkpoint.c
    •       fixed mpi hang/crash with separate pme nodes and dd nodes without charges
    •       pdb2gmx now prints the force field dir before the selection and checks for multiple dirs with the same name
    •       removed the pdb2gmx -cwd option and updated the pdb2gmx description
    •       fixed pdb2gmx behavior for nearly matching residue names and made the matching much stricter
    •       updated gmx_membed.c for a VV update
    •       fixed bug in search_rtp introduced in previous commit
    •       fixed pdb2gmx using start name iso end name for C-terminus
    •       pdb2gmx now only allows a mismatch of a sign (iso any character) at the end of a residue and rtp name
    •       fixed bug that caused corrupted checkpoint file
    •       make cmake install a CMakeLists.txt for the template program
    •       split libs in Template.mak
    •       store custom GMX defines in pkgconfig files for autotools
    •       fixed some out of srcdir build issue with cmake and GMXRC
    •       store custom GMX defines in pkgconfig files for cmake
    •       port lib suffixes to cmake
    •       cmake: make demux.pl and xplor2gmx.pl being installed with the right permissions
    •       cmake: add so version to libs
    •       cmake: do not suffix scripts
    •       Fixed threads flags in pc files for autotools
    •       Fixes more misery in function skipstr, where pointers were incremented
    •       Fixed bug 417.
    •       Made genrestr -constr to produce constraints of type 2 that do not generate
    •       Renamed intel syntax assembly files to avoid double extensions
    •       Changes to make Cmake work under windows again
    •       Moved four more SSE assembly files to avoid double extensions with intel syntax
    •       Cmake and Nasm support for windows
    •       Fixed SSE kernels in double precision for Cmake, working in windows+osx, and fixed MSVC SSE intrinsics problems
    •       Removed extra TER records after chains we think are polymers - this easily
    •       Fixed checkpoint problem in 32 bits. We should always check for SIZEOF_GMX_OFF_T, since the implementation _might_ use long int instead of off_t on some hosts.
    •       Fixed compiler errors for MSVC inline intrinsics and added a test to detect incorrect CMake OS X configurations.
    •       Fixed a naming error introduced yesterday in 32bit SSE GB kernel 430
    •       Fixed typo to detect both x86_64->i386 and i386->x86_64 OS X architecture changes in cmake
    •       Renamed SSE2 x86-64 asm test file to be consistent with other archs
    •       Updated autoconf to work with renamed SSE2 x86-64 asm test file name too
    •       Added ia32 all-vs-all kernels
    •       Added double precision SSE2 generalized born kernels. Note that these now _compile_, but they are not yet tested for accuracy (coming next week)
    •       Fixed potential error in coulomb energy, and maybe segfaults for small molecules in all-vs-all kernels
    •       Copied all-vs-all change from x86-64 to ia32 kernels too
    •       Deprecated -ins option to g_hbond since nobody seems to support it.
    •       Worked around an internal compiler error for MSVC when double was used with SSE2
    •       Fixed 64-bit bug in SSE assembly (only visible with nasm)
    •       Fixed previous nasm-segv bug for intel-syntax SSE in the double precision SSE2 kernels too
    •       Enabled double precision all-vs-all kernels. Tested and appears to work for normal interactions, GB testing in progress.
    •       Fix to write GB and surface energy to separate terms, rather than putting everything in GB12
    •       Modified improper torsion atom order in Amber TRP residues to conform to original amber10
    •       Modified atom order in Amber nucleotide improper torsions to match amber 10
    •       Updated GB SSE2 kernels, testing in progress now...
    •       Double precision SSE2 kernels for Generalized Born fixed & validated
    •       Fixed a chain rule error in double prec. SSE2 GB for OBC algorithm
    •       Upgraded to latest autoconf platform detection scripts
    •       Fixed so Fortran kernels work again
    •       Dont write nonpolar surface energy to energy file if we dont use GB
    •       Fixed a minor bug that caused Fortran builds to fail. File mode for xdr3dfcoord() is now derived from the XDR struct.
    •       Fixed an uninitialized variable bug
    •       Fixed a bug for GB OBC born radius calculation in SSE2 double precision
    •       Fixed synchronization counter update for f77 kernels
    •       Added F77 kernel setup headers
    •       Amber force fields now pass validation. Beta status removed.
    •       Removed some unnecessary #ifdefs from string2.h; all our string routines should be prefixed with gmx_.
    •       Cleaned up all installed headers to remove strict dependence on config.h. Important settings are now detected directly from the compiler and environment, and non-important stuff has been removed or moved to source files.
    •       Fixed naming problems for double precision Fortran kernels
    •       Replaced testing of git version with testing for features
    •       Fixed stupid mistake where a statement was placed before declarations.
    •       Replaced all occurences of str(n)casecmp with gmx_str(n)casecmp.
    •       Copied SSE intrinsics kernels from x86-64 to ia32
    •       Fixed two more instances of strcasecmp->gmx_strcasecmp
    •       Fixed an unsigned/signed integer comparison
    •       Fixed uninitialized variable error in GB kernel with tabulated LJ
    •       Updated intel syntax x86-64 asm files to also support MS win64 call convention (ifdef, so they should still work for linux/mac too)
    •       Re-added openmm paper
    •       Made sure all source files have some copyright header and include config.h
    •       Added missing header include
    •       Changed bool to signed integer instead of unsigned char.
    •       Forgot to actually do the char->int change...
    •       Fixed include path in vmdio.h
    •       g_kinetics removed from automatically built programs since it is not functional in a default build without GSL.
    •       Removed useless g_logo and g_highway programs from default build
    •       Updated manpages for 4.5 release
    •       Updated scripts to produce 4.5 man pages
    •       Changed version to beta4
    •       Fix for warning in ngmx makefile
    •       Updated manual pages, now with correct version (4.5) as a bonus...
    •       Updated html documentation for release 4.5
    •       Made /usr/local/gromacs default installation path in cmake too
    •       Updated completions for 4.5 release
    •       Revert "Made pdb2gmx be slightly more helpful when using AMBER forcefields"
    •       true/false input settings should be called bool instead of gmx_bool
    •       Modified pdb2gmx to not accept extra hydrogen atoms at the N-terminus
    •       Added PBC checking patch to g_cluster from Alexey Shvetsov (Bugzilla 526)
    •       Fixed pointer typo in patch from Alexey Shvetsov
    •       Modified pdb2gmx to automatically pick the force field from the current directory
    •       Fixed first statemement occuring before variable declarations in gmx_pme_error()
    •       Dont write EOF warnings to stdout every time we checkpoint if the file size==0
    •       Add current path (./) to topol.top include when force field was local
    •       Fixed another uninitialized variable warning in gmx_energy.c
    •       Fixed gmxcpp to always use unix path separators in internal names (just like cpp)
    •       Two spelling fixes in comment and output
    •       Made pdb2gmx be slightly more helpful when using AMBER forcefields
    •       Fixed leak from unclosed directory handles when pdb2gmx was scanning
    •       Clarified documentation about when gen_vel generates velocities
    •       Fixed HTML documentation to use proper '&ge', not '&gt=', etc.
    •       Made the description of ld_seed and gen_seed seed generation more accurate and maintainable.
    •       Spelling fixes in pdb2gmx documentation
    •       Eliminated some commented out code.
    •       First pass at getting VV / v-rescale formula correct.
    •       Trying to get vscale working with vv.
    •       Changed the way energy conservation bookeeping is done.
    •       Proposed fix for v-rescale and berendsen for velocity verlet by rescaling at the time of coupling.
    •       Fixed bug with md-vv and with v-rescale
    •       Fix for readir.c so that nstpcouple and nsttcouple are the same when using MTTK for pressure.
    •       Additional changes for setting nsttcouple
    •       Additional fixes to the nsttcouple and nstpcouple working correctly for trotter decompositions.
    •       Added CT3 termini and minor edit in doc file.
    •       fixed spelling mistake introduced by 303d4543
    •       Fix two Windows futil bugs:
    •       Use always DIR_SEPARATOR
    •       Parenthesis around comparisons and no <= or >= for xlc
    •       Fix for CMake builds so that they don't fail even when version.c hasn't been generated.
    •       CMake builds now install GMXRC* files.
    •       Added a new file INSTALL.cmake  with installation instructions for using CMake.
    •       Fixed broken linking with single precision fftw3 in CMake.
    •       Updated the CMake scripts for finding CUDA, LibXml2 and MPI with the latest 2.8.2 modules.
    •       Warnings about using broken MPI implementations.
    •       Fixed a reverted version string in configure.ac
    •       OpenMM: added support for AmberFF proper/improper torsion potentials.
    •       Added support for improper dihedrals needed for CHARMM in OpenMM
    •       Removed the nb_kernel4xx_intel_syntax.c entries from the makefiles.
    •       Preserve the .pl extentions to scripts.
    •       Fixed the execution order in OpenMM so that the generated trajectory frames correspond to the CPU ones.
    •       Enable the Reference platform for OpenMM.
    •       Fixed a typo about non-existing macro in OpenMM
    •       Redefine the default boolean type to gmx_bool.
    •       Removed the unnecessary hacks from some boolean statements.
    •       Fixed hardcoded OpenMM library name.
    •       Added the g_pme_error tool from Florian Dommert. Thanks!
    •       Modified the OpenMM wrapper interface to support the strange CUDA platform implementation
    •       Cmake now honors CFLAGS/CXXFLAGS as much as it can.
    •       C++ type fixes in thread_mpi atomics.
    •       Fixed an issue with gmx_copy_file that would allow copies of empty files.
    •       Moved the OS-dependent part of gmx_fio_fsync() to futil.c
    •       Fixed xdr3dfcoord thread safety issues.
    •       fsync fix for FAH core.
    •       Fixed thread_mpi inline assembly issue and non-optimized compiles.
    •       Cmake tests for SIGUSR1
    •       Fixed get_libdir() PATH search.
    •       Added support for new mdp options controlling free energy perturbation output.
    •       Completely removed all occurrences of 'inline' for xlc on ppc in thread_mpi.
    •       More xlc ppc changes to thread_mpi
    •       Enabled gcc atomic intrinsics for gcc on ppc.
    •       Modified memory barrier on ppc/xlc.
    •       Another try with xlc/ppc atomics..
    •       Free energy writing to ener.edr and four new options work
    •       g_bar reads dhdl.xvg files without derivatives.
    •       derivative histograms are now written in both positive and negative directions.
    •       Free energy histogram bug fixes.
    •       gmx_bar now works with derivative histogram sets.
    •       More documentation for g_bar.
    •       Fixed begin and end times in g_bar
    •       Fixed non-interactive stdin selection parsing.
    •       Fixed CMake build with CMake 2.6.2.
    •       Cosmetic fixes for selection parsing.
    •       Fixed valgrind warnings and a segfault in pdb2gmx.
    •       fixed apme bug that caused slightly incorrect results when the grid was not divisible by the number of pme nodes in x or y
    •       reenabled the pdb2gmx force field sorting
    •       fixed too permissive check for pdb2gmx warning about unknown rtp names
    •       renamed oplsaa HISA to HISD and HISB to HISE in all files (before done only in the rtp file)
    •       added Amber terminal His rtp names to residuetypes.dat
    •       pdb2gmx can now rename terminal rtp entries with rtp iso gmx residue names when an env.var. is set
    •       fixed pdb2gmx not automatically changing termini rtp entries for Amber FF's
    •       turned on pdb2gmx Amber rtp renaming for pdb input with Amber residue names on by default

    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 22:04, 27 Aug 2010 by rossen