GROMACS 2019.5 release notes#
This version was released on December 23rd, 2019. These release notes document the changes that have taken place in GROMACS since the previous 2019.4 version, to fix known issues. It also incorporates all fixes made in version 2018.8 and earlier, which you can find described in the Release notes.
Fixes where mdrun could behave incorrectly#
Fix use of uninitialized data on PME only ranks#
When building GPU enabled versions of GROMACS with clang as either host only or host and device side compiler, PME datastructures could be left uninitialized, leading to the use of random values for LJ PME energies, virial and pressure.
The effect of this bug was that the potential and total energy could be wrong, but not the Coulomb mesh energy. This didn’t affect sampling. The pressure could also be wrong, which would affect sampling when pressure coupling is used, but likely the simulation would explode after a few steps.
This doesn’t seem to have affected versions of GROMACS built with gcc as the host side compiler.
Fix out of range memory access with free-energy calculations#
With free-energy calculations not using lambda states, an output buffer would be accessed one element beyond it’s allocated size. We don’t expect this to have caused incorrect results, but a memory checker would complain.
Work around broken Apple Clang compiler in Mac OS Catalina#
In Mac OS Catalina, the default XCode compilers checks and enforces stack alignment. This would have been a good idea if Apple itself did not ship a C library that violates the stack alignment with AVX instructions are enabled.
Fix error with intermolecular interactions and domain decomposition#
With intermolecular interactions at distances longer than the cutoff and domain decomposition, mdrun could exit with an error message about missing interactions.
Fix issues with AWH with pull-geometry ‘direction’ to be periodic#
Removed fatal error with AWH with periodic pull-geometry ‘direction’ when the distance was within 2% of half the box size. Changed an assertion failure when the AWH interval was larger than the box size to a fatal error. Clarified the documentation for pull geometry ‘direction-periodic’.
Remove assertion failure with AWH when not using the initial stage#
Make histogram output clearer#
Output gave number of events included in histogram bar as a.u., which was not clear for users.
Fix dihedral angle calculation near 180 degree boundary#
The analysis tools could incorrectly calculate properties of torsion angles and their averages when close to the -180 or 180 degree boundary.
Remove problematic output of gmx angle tool#
It could happen that the calculation of the standard deviation for angles caused a divide by zero error for empty populations. Because this standard deviation was meaningless, it has been removed.
Fixes that affect portability#
Check that libhwloc headers and runtime match#
It could happen that the libhwloc headers and library detection would lead to a mismatch at compile or runtime that could cause cryptic crashes while using mdrun.
Fix .gro file formatting with large boxes#
The GROMACS manual says the box components in the .gro file format are separated by spaces. But no space was printed when a box component, except for the first, was 1000 nm or larger or an off-diagonal component was -100 nm or smaller. Now at least one space is always printed. Content that was written in a way that already had at least one space between components is unchanged. Existing parsers that conform to the documentation and expect whitespace separation will continue to work in all cases.
Fix duplicate PDB CONECT record output#
PDB “CONECT” record output was duplicated in some instances. Since GROMACS does not use these anywhere, analysis was not affected. The behavior is now fixed.
Fix performance issue with bonded interactions in wrong GPU stream#
This could lead to a significant loss in performance.