Gromacs

News

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.

20 Aug 2009

Gromacs has been ported to run on Microsoft Windows HPC Server 2008 thanks to the hard work of Dr. Roberto Lins's group at the Pacific National Northwest Laboratory. The binary and the source code are available for download from the MS Windows contributions section.