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

[Amit Choubey]

Hi Rossen,

Could you send me a documentation of memory usage by gromacs-4.5-beta1. I
would like to know the maximum no. of atoms that we can simulate on our
university supercomputer.

amit

On Fri, Jul 30, 2010 at 12:20 PM, Rossen Apostolov <
rossen.apostolov at cbr.su.se> wrote:

>
> After months of hard work and 2449 patches, the new gromacs-4.5-beta1 is
> out!
>
> 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
> information.
>
>
> 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 simulations.
>    - 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 required)
>    - 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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