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Friday, 04 January 2008 |
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Berk Hess has just published the details of the parallel constraint solver (P-LINCS) that is implemented in GROMACS 4.0, in conjunction with the new domain decomposition scheme. This is the first parallel constraint solver available in a software package for MD simulations, allowing the use of 4-5 fs time steps when combined with virtual sites. When only constraints on bonds involving hydrogen atoms are used, as implemented in most other packages, time steps should not be larger than 1 fs, and hence the P-LINCS algorithm gives GROMACS an increased competetive advantage over other packages. |
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Generating REMD Temperatures |
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Thursday, 03 January 2008 |
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Alexandra Patriksson & David van der Spoel have written a temperature generator algorithm for replica exchange molecular dyamics simulations. The algorithm is available as a webserver and it generates temperatures based on your simulation details. Please try it out and send us some feedback at the address mentioned on the website. |
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Saturday, 15 December 2007 |
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A developer meeting took place 13-14 december in Groningen, The Netherlands, hosted by Siewert-Jan Marrink. The three core developers, Berk, Erik and David were there along with local participants and people from Germany and Canada. The main topic was multiscale simulations, and routes towards inclusion of this kind of models in GROMACS were discussed. Some of these will show up in the upcoming 4.0 release, spring 2008. |
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Sunday, 30 September 2007 |
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Last Friday, Sept. 28th, the latest stable release of GROMACS was updated to version 3.3.2. It includes a lot of small bugfixes, and is the recommended version for production simulations. |
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Wednesday, 12 September 2007 |
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The GROMACS code is now part of the SPEC 2006 benchmark system for CPUs . That means hardware vendors that want to show off their hardware run GROMACS as a part of their benchmarks and some of them tune hardware and/or compilers to get better results. Look for test 435.gromacs to compare your favorites hardware. Note though, that for the benchmark we were not allowed to use assembly code, so the results you see there are in C-code. As a result the numbers are not representative of true GROMACS performance. |
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