<div dir="ltr"><span id="docs-internal-guid-a0e5cac7-e961-fecf-e87a-cf72787903e6"><p dir="ltr" style="line-height:1.15;margin-top:0pt;margin-bottom:0pt"><span style="font-size:15px;font-family:Arial;color:rgb(0,0,0);vertical-align:baseline;white-space:pre-wrap;background-color:transparent">Hi GROMACS users,</span><span style="font-size:15px;font-family:Arial;color:rgb(0,0,0);vertical-align:baseline;white-space:pre-wrap;background-color:transparent"><br class="">
</span><span style="font-size:15px;font-family:Arial;color:rgb(0,0,0);vertical-align:baseline;white-space:pre-wrap;background-color:transparent"><br class=""></span><span style="font-size:15px;font-family:Arial;color:rgb(0,0,0);vertical-align:baseline;white-space:pre-wrap;background-color:transparent">The official release of GROMACS 5.0 is available!</span><span style="font-size:15px;font-family:Arial;color:rgb(0,0,0);vertical-align:baseline;white-space:pre-wrap;background-color:transparent"><br class="">
</span><span style="font-size:15px;font-family:Arial;color:rgb(0,0,0);vertical-align:baseline;white-space:pre-wrap;background-color:transparent"><br class=""></span><span style="font-size:15px;font-family:Arial;color:rgb(0,0,0);vertical-align:baseline;white-space:pre-wrap;background-color:transparent">What new things can you expect?</span></p>
<br><p dir="ltr" style="line-height:1.15;margin-top:0pt;margin-bottom:0pt"><span style="font-size:15px;font-family:Arial;color:rgb(0,0,0);vertical-align:baseline;white-space:pre-wrap;background-color:transparent">* GROMACS now uses a combination of *C++98* and C99, so you will need a working C++ compiler that is intended to work with your C compiler</span></p>
<p dir="ltr" style="line-height:1.15;margin-top:0pt;margin-bottom:0pt"><span style="font-size:15px;font-family:Arial;color:rgb(0,0,0);vertical-align:baseline;white-space:pre-wrap;background-color:transparent"><br class="">
</span><span style="font-size:15px;font-family:Arial;color:rgb(0,0,0);vertical-align:baseline;white-space:pre-wrap;background-color:transparent">* Building GROMACS now requires *CMake version 2.8.8*, which will mean some of you will need to update your version in order to build GROMACS.</span></p>
<br><p dir="ltr" style="line-height:1.15;margin-top:0pt;margin-bottom:0pt"><span style="font-size:15px;font-family:Arial;color:rgb(0,0,0);vertical-align:baseline;white-space:pre-wrap;background-color:transparent">* The native GPU port available in GROMACS 4.6 supports a wider range of simulation types, and now requires CUDA 4.0</span></p>
<br><p dir="ltr" style="line-height:1.15;margin-top:0pt;margin-bottom:0pt"><span style="font-size:15px;font-family:Arial;color:rgb(0,0,0);vertical-align:baseline;white-space:pre-wrap;background-color:transparent">* The *Verlet cut-off scheme is now the default* in GROMACS. One of our design principles is that GROMACS will do correct simulations by default, and the use of this scheme makes that easy and fast. The group cut-off scheme will be removed in a future version, so start planning for that!</span><span style="font-size:15px;font-family:Arial;color:rgb(0,0,0);vertical-align:baseline;white-space:pre-wrap;background-color:transparent"><br class="">
</span><span style="font-size:15px;font-family:Arial;color:rgb(0,0,0);vertical-align:baseline;white-space:pre-wrap;background-color:transparent"><br class=""></span><span style="font-size:15px;font-family:Arial;color:rgb(0,0,0);vertical-align:baseline;white-space:pre-wrap;background-color:transparent">* You can now treat *Lennard-Jones interactions with PME*, which is expected to provide a much better treatment of spatially heterogeneous long-ranged dispersion interactions at cost comparable to that of a cutoff. LJPME is supported for both cut-off schemes, and almost all kinds of simullations</span><span style="font-size:15px;font-family:Arial;color:rgb(0,0,0);vertical-align:baseline;white-space:pre-wrap;background-color:transparent"><br class="">
</span></p><p dir="ltr" style="line-height:1.15;margin-top:0pt;margin-bottom:0pt"><span style="font-size:15px;font-family:Arial;color:rgb(0,0,0);vertical-align:baseline;white-space:pre-wrap;background-color:transparent">* GROMACS deploys the Random123 stateless random-number generator</span></p>
<br><p dir="ltr" style="line-height:1.15;margin-top:0pt;margin-bottom:0pt"><span style="font-size:15px;font-family:Arial;color:rgb(0,0,0);vertical-align:baseline;white-space:pre-wrap;background-color:transparent">* GROMACS now uses the stochastic dynamics (sd1) integrator of Goga & Berendsen</span></p>
<br><p dir="ltr" style="line-height:1.15;margin-top:0pt;margin-bottom:0pt"><span style="font-size:15px;font-family:Arial;color:rgb(0,0,0);vertical-align:baseline;white-space:pre-wrap;background-color:transparent">* GROMACS tools are now bundled together into *just two binaries* - mdrun and gmx. The latter contains most of the tools familiar to you, perhaps with new names, and a couple of new ones. For the time being, the install procedure will also create symbolic links so that your old scripts will keep working for a time, but these will go away at some future point!</span><span style="font-size:15px;font-family:Arial;color:rgb(0,0,0);vertical-align:baseline;white-space:pre-wrap;background-color:transparent"><br class="">
</span><span style="font-size:15px;font-family:Arial;color:rgb(0,0,0);vertical-align:baseline;white-space:pre-wrap;background-color:transparent"><br class=""></span><span style="font-size:15px;font-family:Arial;color:rgb(0,0,0);vertical-align:baseline;white-space:pre-wrap;background-color:transparent">* There is support for the new TNG compressed trajectory format</span><span style="font-size:15px;font-family:Arial;color:rgb(0,0,0);vertical-align:baseline;white-space:pre-wrap;background-color:transparent"><br class="">
</span><span style="font-size:15px;font-family:Arial;color:rgb(0,0,0);vertical-align:baseline;white-space:pre-wrap;background-color:transparent"><br class=""></span><span style="font-size:15px;font-family:Arial;color:rgb(0,0,0);vertical-align:baseline;white-space:pre-wrap;background-color:transparent">* GROMACS contains a feature for "computational electrophysiology" simulations, to simulate a steady-state ion concentration difference between compartments of a double membrane</span></p>
<br><p dir="ltr" style="line-height:1.15;margin-top:0pt;margin-bottom:0pt"><span style="font-size:15px;font-family:Arial;color:rgb(0,0,0);vertical-align:baseline;white-space:pre-wrap;background-color:transparent">* GROMACS supports some special interactions for coarse-grained interactions with Martini force fields</span><span style="font-size:15px;font-family:Arial;color:rgb(0,0,0);vertical-align:baseline;white-space:pre-wrap;background-color:transparent"><br class="">
</span></p><p dir="ltr" style="line-height:1.15;margin-top:0pt;margin-bottom:0pt"><span style="font-size:15px;font-family:Arial;color:rgb(0,0,0);vertical-align:baseline;white-space:pre-wrap;background-color:transparent">* GROMACS support for Interactive Molecular Dynamics (IMD)</span></p>
<p dir="ltr" style="line-height:1.15;margin-top:0pt;margin-bottom:0pt"><span style="font-size:15px;font-family:Arial;color:rgb(0,0,0);vertical-align:baseline;white-space:pre-wrap;background-color:transparent"><br class="">
</span><span style="font-size:15px;font-family:Arial;color:rgb(0,0,0);vertical-align:baseline;white-space:pre-wrap;background-color:transparent">* A handful of the tools have been re-implemented using a *new C++ analysis framework*, which we hope will provide a better platform for maintaining and adding to their functionality in the future. </span></p>
<p dir="ltr" style="line-height:1.15;margin-top:0pt;margin-bottom:0pt"><span style="font-size:15px;font-family:Arial;color:rgb(0,0,0);vertical-align:baseline;white-space:pre-wrap;background-color:transparent"><br class="">
</span><span style="font-size:15px;font-family:Arial;color:rgb(0,0,0);vertical-align:baseline;white-space:pre-wrap;background-color:transparent">* There is an enhanced testing suite, with *unit tests* for most new C++ code.</span></p>
<br><p dir="ltr" style="line-height:1.15;margin-top:0pt;margin-bottom:0pt"><span style="font-size:15px;font-family:Arial;color:rgb(0,0,0);vertical-align:baseline;white-space:pre-wrap;background-color:transparent">* There is preliminary support for Intel Xeon Phi (only in native mode, and performance will only be slightly improved)</span><span style="font-size:15px;font-family:Arial;color:rgb(0,0,0);vertical-align:baseline;white-space:pre-wrap;background-color:transparent"><br class="">
</span></p><p dir="ltr" style="line-height:1.15;margin-top:0pt;margin-bottom:0pt"><span style="font-size:15px;font-family:Arial;color:rgb(0,0,0);vertical-align:baseline;white-space:pre-wrap;background-color:transparent">* GROMACS has removed support for particle decomposition - the simulation types that required it are now limited to a single MPI rank (but perhaps multiple OpenMP threads)</span></p>
<br><p dir="ltr" style="line-height:1.15;margin-top:0pt;margin-bottom:0pt"><span style="font-size:15px;font-family:Arial;color:rgb(0,0,0);vertical-align:baseline;white-space:pre-wrap;background-color:transparent">Please see the link to the release notes below for more details. All the content of GROMACS 4.6.6 (whose release is imminent) is present, apart from features that have been removed.</span><span style="font-size:15px;font-family:Arial;color:rgb(0,0,0);vertical-align:baseline;white-space:pre-wrap;background-color:transparent"><br class="">
</span><span style="font-size:15px;font-family:Arial;color:rgb(0,0,0);vertical-align:baseline;white-space:pre-wrap;background-color:transparent"><br class=""></span><span style="font-size:15px;font-family:Arial;color:rgb(0,0,0);vertical-align:baseline;white-space:pre-wrap;background-color:transparent">You can find the code, manual, release notes, installation instructions and test suite at the links below.</span><span style="font-size:15px;font-family:Arial;color:rgb(0,0,0);vertical-align:baseline;white-space:pre-wrap;background-color:transparent"><br class="">
</span><span style="font-size:15px;font-family:Arial;color:rgb(0,0,0);vertical-align:baseline;white-space:pre-wrap;background-color:transparent"><br class=""></span><span style="font-size:15px;font-family:Arial;color:rgb(0,0,0);vertical-align:baseline;white-space:pre-wrap;background-color:transparent"><a href="ftp://ftp.gromacs.org/pub/gromacs/gromacs-5.0.tar.gz">ftp://ftp.gromacs.org/pub/gromacs/gromacs-5.0.tar.gz</a></span></p>
<p dir="ltr" style="line-height:1.15;margin-top:0pt;margin-bottom:0pt"><span style="font-size:15px;font-family:Arial;color:rgb(0,0,0);vertical-align:baseline;white-space:pre-wrap;background-color:transparent"><a href="ftp://ftp.gromacs.org/pub/manual/manual-5.0.pdf">ftp://ftp.gromacs.org/pub/manual/manual-5.0.pdf</a></span></p>
<p dir="ltr" style="line-height:1.15;margin-top:0pt;margin-bottom:0pt"><span style="font-size:15px;font-family:Arial;color:rgb(0,0,0);vertical-align:baseline;white-space:pre-wrap;background-color:transparent"><a href="http://www.gromacs.org/About_Gromacs/Release_Notes/Versions_5.0.x#Release_notes_for_5.0">http://www.gromacs.org/About_Gromacs/Release_Notes/Versions_5.0.x#Release_notes_for_5.0</a></span></p>
<p dir="ltr" style="line-height:1.15;margin-top:0pt;margin-bottom:0pt"><span style="font-size:15px;font-family:Arial;color:rgb(0,0,0);vertical-align:baseline;white-space:pre-wrap;background-color:transparent"><a href="http://www.gromacs.org/Documentation/Installation_Instructions_for_5.0">http://www.gromacs.org/Documentation/Installation_Instructions_for_5.0</a></span></p>
<p dir="ltr" style="line-height:1.15;margin-top:0pt;margin-bottom:0pt"><span style="font-size:15px;font-family:Arial;color:rgb(0,0,0);vertical-align:baseline;white-space:pre-wrap;background-color:transparent"><a href="http://gerrit.gromacs.org/download/regressiontests-5.0.tar.gz">http://gerrit.gromacs.org/download/regressiontests-5.0.tar.gz</a></span></p>
<br><p dir="ltr" style="line-height:1.15;margin-top:0pt;margin-bottom:0pt"><span style="font-size:15px;font-family:Arial;color:rgb(0,0,0);vertical-align:baseline;white-space:pre-wrap;background-color:transparent">Happy simulating!</span></p>
<br><p dir="ltr" style="line-height:1.15;margin-top:0pt;margin-bottom:0pt"><span style="font-size:15px;font-family:Arial;color:rgb(0,0,0);vertical-align:baseline;white-space:pre-wrap;background-color:transparent">Mark Abraham</span></p>
<span style="font-size:15px;font-family:Arial;color:rgb(0,0,0);vertical-align:baseline;white-space:pre-wrap;background-color:transparent">GROMACS development manager</span></span><br></div>