GROMACS 2016.2 Release Notes#
This version was released on February 7, 2016. These release notes document the changes that have taken place in GROMACS since version 2016.1 to fix known issues. It also incorporates all fixes made in version 5.1.4 and several since.
Fixes where mdrun could behave incorrectly#
Add grompp check for equipartition violation risk for decoupled modes#
When atoms involved in an angle with constrained bonds have very different masses, there can be very weakly coupled dynamics modes. Default mdp settings are often not sufficiently accurate to obtain equipartitioning. This change adds a grompp check for this issue.
Part of Issue 2071
Disallow overwriting of dihedral type 9#
It is no longer allowed to repeat blocks of parameter of multiple lines for dihedrals of type 9. It is also no longer allowed to override parameters or dihedrals of type 9. Both are too complex to properly check. It is still allowed to repeat parameters blocks consisting of a single line. Repeating a block with the same parameters would lead to incorrect dihedral potentials and forces.
Fixed flat-bottom position restraints + DD + OpenMP#
A (re)allocation was missing, causing a crash.
Fixed multi-domain reruns#
Old code cleanup led multi-domain rerun to crash because it failed to consider logic separated over two places.
Fixes for mdrun performance issues#
Corrected CUDA sm_60 performance#
The kernel launch now suits the SM size of the GP100 architecture.
Fixed some FFT handling in cross-corrrelation calculations#
An array of complex number was created as an array of pointers and then passed to gmx_fft_1d. This does not work.
Fixed gmx rmsf -q -oq#
This led to the PDB file containing B-factors using coordinates based on those from the -s file, rather than -q file. gmx rmsf -oq was otherwise fine.
Fixed crash in gmx order#
gmx order used a cumbersome floating point method to compute a histogram, leading to an index value that could be negative.
Fixed minor trjconv bug#
gmx trjconv -novel -f in.pdb -o out.pdb probably works better now.
Fixed time label print in gmx vanhove#
Handled issuing warnings correctly in xpm2ps and membed#
The code should not (over)write the output file before checking for errors. For membed, it is useful to require the user to fix issues in their input file before we unilaterally over-write it.
Corrected documentation about eigenvalue handling#
Some file format docs were out of step with the implementation in eigio.cpp.
The behaviour of gmx anaeig -eig -eig2 was not properly documented.
Made editconf B-factor attachment more useful in practice#
B-factor values will be added to residues unless an index is larger than the number of residues or an option is specified. Protein residue indices can start from any number and, in case they start from a large number, there is no way to add B-factor values to residues.
This patch changes it to add B-factor values to residues unless the number of B-factor values is larger than the number of residues.
Fixed possible memory error with long selections#
If a selection was more than 1000 characters long and there was a whitespace exactly at the 1000 point, a buffer overflow could occur. Replaced the buffer with std::string, simplifying the code significantly.
Fixed use of position variables with plus/merge#
If a selection contained a position variable (e.g., ‘com of …’) that was used more than once, and at least one of those uses was with plus/merge, there were out-of-bounds memory writes. This was caused by the internal position structure not getting fully initialized. Incomplete initialization happens in all contexts with such variables, but only plus/merge (and possibly permute) actually use the values that remained uninitialized, which caused them to incorrectly compute the amount of memory required to store the result.
Made several minor improvements to documentation and messages to users#
In particular, for selections:
Explained resindex and resnr keywords in selection help.
Explained how selection-enabled tools treat -s and -f input files.
Clarified use of tau-p and pcoupltype#
grompp used to permit the erroneous “tau-p = 5 5”. This does not reflect that only one time constant is permitted for pressure coupling (unlike group-based temperature coupling). The recent fix for Issue 1893 leads to the user receiving a grompp warning, so this improves the docs to make clear that pressure coupling is different.
Fixed x86 conditional on IBM s390x#
The CpuInfoTest.SupportLevel test fails on IBM s390x because wrong condition was used.
Build system enhancements#
Fixed compilation with CMAKE_CXX_FLAGS=”-Wall -Werror”#
Stopped trying to use objdump –reloc in the build system on Mac#
Recent Xcode objdump does not support –reloc.
The warning that is based on the output of running objdump was only implemented to work on Linux-like things, so should not spam the cmake output on other platforms.
Improved the support for plugin loading in the build system#
The mdrun-only and prefer-static-libs builds set the default for BUILD_SHARED_LIBS to off, which silently disabled plugin support for things like VMD-based I/O handling.
Converted GMX_LOAD_PLUGINS to tri-state ON/OFF/AUTO so that if the preconditions for support are not met we can have suitable behaviour in each case.
Turn off hwloc support when static lib found#
Hwloc dependencies are not resolved at CMake time when static libwloc.a is detected and in most of these cases link-time errors will prevent building GROMACS. As it is hard for a user to know how to solve such cryptic errors and hwloc is not a required dependency, we turn off hwloc support when a static lib is detected. The user can override this on the cmake command line.
Fixed build with GMX_EXTERNAL_TNG=ON#
House-keeping that reduces users’ problems#
Mdrun prints invalid performance data less often#
If mdrun finished before a scheduled reset of the timing information (e.g. from mdrun -resetstep or mdrun -resethway), then misleading timing information should not be reported.
Related, the default reset step for gmx tune_pme was increased to 1500.
Added a runtime check for number of threads in bonded code#
Replaced a debug assertion on the number of OpenMP threads not being larger than GMX_OPENMP_MAX_THREADS by fatal error. But since the listed-forces reduction is actually not required with listed forces, these are now conditional and mdrun can run with more than GMX_OPENMP_MAX_THREADS threads.
Fixed integer narrowing in TNG reading for long trajectories#
Reading of TNG trajectories with sufficiently large numbers of frames could truncate integers used for frame numbers. Fixed to use 64-bit integers as originally intended.
Fixed logic of TRR reading#
When reading a trr file, reaching the end of the file was indistinguishable from a reading error or a magic-number error. This is now fixed, restoring the intended behaviour in each case.