QUICK LINKS: BINARIES SEARCH THE MAILING LIST ONLINE MANUAL SOURCE CODE ACCESS
Sticky: Can't Post to the mailing list? Read the 'important information' section on the mailing list page.
Send a mail to email if you want to be registered as a contributor and be able to upload files or modify the webpage content.
News
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 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!
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.
