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.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! > > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php >
-- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php