[gmx-users] GROMACS-4.5-beta1 is out!

Rossen Apostolov rossen.apostolov at cbr.su.se
Fri Jul 30 21:20:38 CEST 2010

After months of hard work and 2449 patches, the new gromacs-4.5-beta1 is 

It is full of many new and exciting features, please try them out!

If something is not working as expected, please send a mail or file a 
bugzilla report.

For developers: there is a new branch for stable releases called 
"release-4-5-patches". Bugfixes should be applied there **first**, and 
if needed, merged from that branch into the master after the fix. See 
http://www.gromacs.org/Developer_Zone/Git/Git_Tutorial#Bugfixes for more 

New features:

    * 2D decomposition support for PME: improved load balancing with up
      to 40% overall performance improvement for large systems.
    * Memory usage is improved for very large systems, allowing
      simulations of >100 million atoms.
    * Running on multi-core nodes now automatically uses threads for
      domain decomposition through the built-in threaded MPI library
    * GPU computing support
    * Check-pointing is made more secure:MD5sum are used to verify that
      all files are correctly in-place before a simulation is appended.
      Output file appending at continuation is turned on by default
    * Full Cmake support. Autoconf/automake will be deprecated after the
      final 4.5 release!
    * Full support for 7 AMBER force fields
    * Support for CHARMM27, including cmap for dihedrals
    * Efficient Generalized-Born implicit solvent support including the
      Still/HCT/OBC-models to compute the Born radii, a novel way of
      tabulating the generalized Born-interaction formula for greater
      speed, and optimized SSE-routines for both cut-off and all-vs-all
    * Support for nucleic acid simulations
    * Support for Velocity-Verlet integrators for reversible T- and
      P-coupling; MTTK pressure control integrators; Nose-Hoover chains
    * Support for Bennett acceptance ratio (BAR) free energy calculations
    * Decoupling group setup for free energy
    * File formats: All GROMACS tools can now read any VMD supported
      trajectory format, without converting trajectory first. (VMD is
    * g_rdf was a little bit enhanced that structure factors can be
      calculated for any system, by supplying the necessary data via
      sfactor.dat. Most of the common atomtypes are already contained,
      but everybody who needs more freedom can enhance the table
    * Library support for "dynamic index groups" based on textual
      selections (experimental feature). See the tool g_select, the
      included template.c, or Doxygen documentation for information on
      how to write analysis tools using the library. Existing tools have
      not (yet) been converted.
    * g_tune_pme: For a given number of processes or threads this tool
      systematically times mdrun with various numbers of PME-only nodes
      and determines which setting is fastest. It also checks whether
      performance can be enhanced by shifting load between the real and
      the reciprocal space part of the Ewald sum.
    * g_membed: a very convenient utility for embedding membrane
      proteins into equilibrated lipid bilayers

Big thanks to all developers, contributors and users!
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