[gmx-users] Gromacs 4.0.3 released

Erik Lindahl lindahl at cbr.su.se
Mon Jan 19 00:33:04 CET 2009

Hi everybody,

We've just released a maintenance version 4.0.3 with a bunch of  
bugfixes and minor enhancements - all issues in bugzilla that had been  
settled to be bugs have been fixed.

You can find it in the usual place:


Some of the fixes are:

* Improved domain decomposition grid and separate PME node setup: it  
will succeed more often and the error messages are clearer.
* mdrun will now tell which atoms are out of range when the domain  
decomposition fails due to too long bonded interaction distances.
* Fixed crashes and hangs which could occur with mdrun -nosum.
* Fixed checkpoint reading which would fail with SD/BD and separate  
PME nodes.
* Fixed normalization of the averages and fluctuations at the end the  
log file by nsteps+1 (was nsteps).
* With mdrun -rerun the averages in the log file and printed by  
g_energy are now correct.
* The mdrun performance print is now correct when the run is  
terminated before the last step.
* In the pull code the sign of the virial contribution is fixed (it  
was incorrect in 4.0 and 4.0.2, it was 0 in version 3.3).
* Made the pull code work again with particle decomposition.
* Several fixes for configuration and compiling on IBM machines,  
especially for the Blue Gene.
* Added some more input checks in grompp and mdrun.
* Fixed gmxlib/mdlib library dependencies for linking with other code.
* Fixed Coulomb forces in nb_generic.c for user modified code.
* Several non-critical fixes in other GROMACS programs.
* Compiler warnings for gcc 4.3 have been addressed
* Compatible with libtool 2.x and automake 1.10.1 (only matters for  



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