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

David van der Spoel spoel at xray.bmc.uu.se
Sat Jul 31 21:45:43 CEST 2010

On 2010-07-31 21.34, Amit Choubey wrote:
> 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.
It is roughly linear with the number of atoms. Just try it.

> amit
> On Fri, Jul 30, 2010 at 12:20 PM, Rossen Apostolov
> <rossen.apostolov at cbr.su.se <mailto: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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David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205.
spoel at xray.bmc.uu.se    http://folding.bmc.uu.se

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