計算化学 ソフトウェア

https://manual.gromacs.org/documentation/2025.2/release-notes/index.html

GROMACS 2025.2 release notes
This version was released on May 12th, 2025. These release notes document the changes that have taken place in GROMACS since the previous 2025.1 version, to fix known issues. It also incorporates all fixes made in version 2024.5 and earlier, which you can find described in the Release notes.

Fixes where mdrun could behave incorrectly
Fix assertion failure with CUDA and HIP builds with empty domains
mdrun could exit with an assertion failure when a domain contained zero atoms.

Issue 5322

Fix mdrun crashes with position restraints + flat-bottomed position restraints + p-coupling with COM refcoord-scaling + OpenMP
This combination can lead to (too) high position restraint forces when OpenMP threads run slightly out of sync. Simulations will have very likely crashed due to too high forces, unless they are very short.

Issue 5337

Fixes for gmx tools
Fix parsing of pdb files with multiple cyclic and acyclic chains
pdb2gmx computed incorrect coordinate distances when checking for cyclicity of the second and later chains in the pdb input file.

Issue 5091

Fix out-of-boundary read in gmx sorient
The outermost (maximum radius) bin in the histograms created for the -o and -no output files from this tool added a value which was read from unallocated memory. Only values in this bin were affected.

Fixes that affect portability
Fixed cross-test for Windows on Linux with Wine
Cross-testing of GROMACS 2025.1 for Windows on Linux with Wine, by setting the CMAKE_CROSSCOMPILING_EMULATOR variable to wine or wine64, could fail due to our tests using CMake generator expressions and ignoring the variable setting. The tests are now executed using the emulator set in the variable.

Issue 5342

Miscellaneous
Intel Xe2/Battlemage documentation
Expanded the documentation and rephrased a misleading error message.

Issue 5330