GROMACS 2018.5 release notes

This version was released on TODO, 2018. These release notes document the changes that have taken place in GROMACS since version 2018.4, to fix known issues. It also incorporates all fixes made in version TODO and earlier, which you can find described in the Release notes.

Fixes where mdrun could behave incorrectly

Fixed numerical derivative for normal-mode analysis with shell code

Due to higher precision needs when using polarizable shell particles the normal mode code did not work reproducibly with shells. In order to fix this the step-size used for numerically computing the Hessian was reduced to near machine precision. The change does not affect the results for non-polarizable systems, such as proteins or small molecules.

Make large PME grids work on GPU

PME grids with size along Z larger than 511 would make mdrun exit with a cryptic CUDA error.


Fix LINCS accuracy with OpenMP when constraint triangles are present

Constraint triangles, which usually only occur when replacing hydrogens by virtual interaction sites in CH3 and NH3 groups, need double the number of iterations as normal constraints. With OpenMP this would only happen when the last OpenMP thread has at least one such triangle. This would cause a slight loss of accuracy in inhomogeneous systems.


Fix acceleration with cos-acceleration

A factor of 2 was missing from the acceleration value, leading to incorrect results when e.g. calculating viscosities.


Fixes for gmx tools

Fixes to improve portability


Warn for problematic coupling times with Nose-Hoover and Parrinello-Rahman

When combining the Nose-Hoover and Parrinello-Rahman coupling algorithms, resonances in the kinetic energy and pressure/volume can appear when the two coupling times involved are similar. Now grompp warns when tau-p is less than two times tau-t.


Fixed efficiency issue with shell code minimization

Code cleanup touching unnecessarily complex code created an efficiency issue. Both the issue and some of the complexity are now fixed.