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