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.aposto...@cbr.su.se <mailto:rossen.aposto...@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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