Gromacs

Gromacs

    Table of contents
    1. 1. News

     

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    get the source code

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    Gromacs users mailing list

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    online manual

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    git repository access

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    The development of Gromacs would not have been possible without generous funding support from the European Research Council, the Swedish Research Council, the Swedish Foundation for Strategic Research, the Swedish National Infrastructure for Computing, and the Swedish Foundation for International Cooperation in Research and Higher Education. Several other grant agencies also provide funding to researchers involved in Gromacs development, in particular NIH and NSF in the US, and the DFG in Germany. For more information, see funding.

    Gromacs is one of the applications that are part of the ScalaLife Competence Center (http://scalalife.eu). The Competence Center is bscalalife3-mini.jpgeing developed as a one-stop-shop for users and developers of Life Science software. Various training events on high-performance computing and optimization techniques for improving scalability and performance will be organized by the center.


    Sticky: Can't Post to the mailing list? Read the 'important information' section on the mailing list page.
                Send a mail if you want to be registered as a contributor and be able to upload files or modify the webpage content.


    News

    October 1, 2014


    GROMACS 5.0.2 is out! Download the source tarball, and check out the release notes.

     

    September 5, 2014


    GROMACS 5.0.1 is out! Download the source tarball, and check out the release notes.

     

    August 29, 2014


    GROMACS 4.6.7 is out! Download the source tarball, and check out the release notes.

     

    July 7, 2014


    GROMACS 4.6.6 is out! Download the source tarball, and check out the release notes.

     

    June 29, 2014


    GROMACS 5.0 is out! Download the source tarball, and check out the release notes.

     

    April 2, 2014


    NVIDIA offers access to the latest and fastest accelerators - the Tesla® K40 GPUs, which offer up to 40% more performance compared to the Tesla K20X. Take a free test-drive with GROMACS here: http://www.nvidia.com/object/gpu-test-drive.html

     

    December 2, 2013


    GROMACS 4.6.5 is out! Download the source tarball, and check out the release notes.

     

    November 13, 2013


    GROMACS 4.6.4 is out! Download the source tarball, and check out the release notes.

     

    July 5, 2013


    GROMACS 4.6.3 is out! Download the source tarball, and check out the release notes.

     

    May 30, 2013


    GROMACS 4.6.2 is out! Download the source tarball, and check out the release notes.

     

    January 21, 2012


    GROMACS 4.6 is out! Download the source tarball, and check out the release notes.

     

    December 22, 2012


    GROMACS 4.6 beta 3 is out! Download the source tarball, and check out the release notes.

     

    December 6, 2012


    GROMACS 4.6 beta 2 is out! Download the source tarball, and check out the release notes.

     

    November 30, 2012


    GROMACS 4.6 beta 1 is out! Download the source tarball, and check out the release notes.

     

    September 21, 2011


    GROMACS is now on Facebook too :) 

     

    September 20, 2011


    New maintenance release: gromacs-4.5.5.tar.gz is available. Here are the release notes.

     

    April 8, 2011


    Updated version 1.1.1 of xdrfile is available for download: ftp://ftp.gromacs.org/pub/contrib/xd...e-1.1.1.tar.gz. It contains compilation fixes and sample Python code for reading xtc files etc. from Python sripts.

     

    March 22, 2011


    Updated version 4.5.4 of the Gromacs manual is available at ftp://ftp.gromacs.org/pub/manual/manual-4.5.4.pdf.

     

    March 21, 2011


    New maintenance release: gromacs-4.5.4.tar.gz. Here are the release notes.

     

    January 6, 2011


    Happy New Year!

    We've been discussing for a while moving away from Bugzilla and start using Redmine for bugtrcking and project management. The latter offers a richer platform that we hope will be more helpful for our collaborative efforts. It is now available at http://redmine.gromacs.org, and the old bugzilla server has been shutdown.

    We've migrated as much of the original bugzilla information as possible. User accounts, bug history, file attachments are all ported. There is still work to be done on organizing and setup so please send us your comments and recommendations.

    IMPORTANT: all user accounts on redmine.gromacs.org have a new default password "redmine" ! (The original password hashes can not be migrated.) Please login and change it as soon as you can! Send a mail if you have any problems.

    Note: with redmine it is possible to host multiple (could be unrelated) projects and sub-projects on the same site. At the moment project "Gromacs" is the top-level one that corresponds to what we had previously in bugzilla. "Bugs" are now referred to as "Issues". Here is a direct link: http://redmine.gromacs.org/projects/gromacs/issues. And you can browse the git repository directly too.

    The road will be probably a little bumpy with the new platform in the beginning but we're hoping for a smoother sail in future!

    November 9, 2010


    New maintenance release is now available: gromacs-4.5.3.tar.gz. Here are the release notes.

     

    October 30, 2010


    A new bugfix release of Gromacs is now available: gromacs-4.5.2.tar.gz. Have a look at the release notes for a list of resolved issues.


    Once again big thanks to all developers for their hard work, and to all users for their contributions!

     

    September 2, 2010


    The new release was a very short lived one - it was missing a few files that broke the CMake build system and now 4.5.1 is out.

     

    September 1, 2010


    It is finally here: Gromacs-4.5 has been just released. All critical issues have been resolved to deliver a stable and powerful package full of many new features.

    Big thanks to all developers and users who made it happen!

    Happy simulating !!!

     

    August 27, 2010


    The last beta release of Gromacs is available for download. The AMBER FF have been validated and are production ready; the GPU code had a serious bug fixed; there is a new tool g_pme_error (it will be incorporated in g_tune_pme soon though). Most of the critical issues since the previous release have been resolved and we expect to have the final 4.5 within a week or so. There will be no more betas.

     

    August 12, 2010


    Now it is possible to search the developers mailing list.

     

    August 10, 2010


    New beta release - gromacs-4.5-beta3. Many bugs have been fixed in this release, mainly double precision support with icc compilers, SSE2. Have a look at the release notes for more details. There are still some issues on Windows platofrms that will be resolved before the final release.

     

    August 2, 2010


    New beta release - gromacs-4.5-beta2. Several important bugs have been fixed in this release, please try it out!

    Also, a new beta release of the GROMACS-GPU is available for download. The new release comes with OpenMM-2.0 and supports pressure coupling.

     


    July 30, 2010

    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 here 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 thread-based parallelization.
    • 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!


    December 6, 2009

    Gromacs-4.0.6 has been released, and a couple of hours later 4.0.7 since the first version tried to build 3DNow instructions by default on 64bit linux (don't worry - there's nothing wrong if you managed to build 4.0.6!) This is a maintenance version that fixes a number of minor bugs reported in bugzilla over the last couple of months.

    29 Sep 2009

    All information from the old wiki site has been moved and reorganized here. Users might find the How-tos and Terminology sections most useful, while developers should check the information available at the Programming Guide section.

    This site uses the Mindtouch wiki engine. It has a very easy and intuitive editor (it shows up when you click on "Edit Page"). Contributors can have a look at the Mindtouch User Guide.

    Now it is possible to search the mailng list archives.

    Using the "Find" form present on every page of the site searches only this site, not the mailing lists.

    The News section was moved as a front page. Often accessed quick links can be found at the top.

    The CVS server can't be accessed anymore, please use tarballs of old releases. The old Gromacs www server (oldwww.gromacs.org) and the old Gromacs wiki server (oldwiki.gromacs.org) have been shut down.

    Page last modified 13:23, 1 Oct 2014 by mabraham