GROMACS 2019.1 release notes

This version was released on February 15, 2019. These release notes document the changes that have taken place in GROMACS since the initial version 2019, to fix known issues. It also incorporates all fixes made in version 2018.5 and earlier, which you can find described in the Release notes.

Fixes where mdrun could behave incorrectly

Fix error with 2D/3D dynamic load balancing

With 2D or 3D domain decomposition with dynamics load balancing, mdrun would exit with the error “The domain decomposition grid as shifted too much ..” when a cell size was limited.

Issue 2830

Fix incorrect LJ repulsion force switching on GPUs

When using a CUDA or OpenCL GPU, the coefficient for the second order term for the LJ repulsion in the force switching function, called ‘A’ in the manual, had the wrong sign. This lead to very small errors in the forces and the pressure. Note that the dispersion force switching was correct. Although the effect on individual atoms pairs was negligible, their combined effect on the pressure could lead to deformation of CHARMM membrane systems, where LJ force switching is regularly applied.

Issue 2845

Fix segmentation fault in mdrun with domain decomposition

Issue 2813

Fix segmentation fault with energy minimization with the group scheme

Using energy minimization in combination with the group cutoff scheme and domain decomposition could lead to a segmentation fault.

Issue 2813

Correct free-energy Delta H output with mass lambda’s

When separate lambda parameters were used for perturbed mass free-energy contributions, these contributions were double counted in the Delta H output used for BAR calculations. Note that dH/dlambda was always correct

Issue 2703 Issue 2849

Prevent mdrun -rerun from writing incorrect free-energy output

Now mdrun -rerun exits with a fatal error when masses or constraints are perturbed. Their contributions to Hamiltonian differences and derivatives were incorrectly set to zero in version 2019.

Issue 2849

Fix possible division by zero in enforced-rotation code

Issue 1431

Fixes for gmx tools

Fix trjconv -ndec

This only works for writing .xtc files. The code and documentation now works correctly with .gro files, which was changed in 2016 release series so that it would only write fixed-width columns.

Issue 2824 Issue 2037

Fix using index file groups when .tpr file not supplied

Selections that use groups from a supplied index file can again be used even when a .tpr file is not supplied.

Issue 2847

Fix tune_pme

The tool did not work due to a file reading error that is fixed now.

Issue 2827

Fixes that affect portability

With MSVC, disabled internal clFFT fallback used for OpenCL support

GROMACS requires MSVC 2017, and the GROMACS OpenCL build requires clFFT. If clFFT is found on the user’s system, then all may be well, but the version of clFFT bundled within GROMACS cannot be built because only MSVC 2010 is supported by clFFT at this time. A configure-time fatal error is now issued in this case.

Issue 2500

Explicitly require 64-bit platforms for OpenCL

A 64-bit OpenCL runtime is required by GROMACS. All known OpenCL implementations on 64-bit platforms are 64-bit (and there are no known 32-bit platforms with 64-bit OpenCL), hence we require a 64-bit platform at configure-time in OpenCL builds. A known unsupported 32-bit platform is ARMv7.


Improved docs for applying electric fields