[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.
> 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
> * 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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