GROMACS 2019.3 release notes

This version was released on June 14, 2019. These release notes document the changes that have taken place in GROMACS since the previous 2019.2 version, to fix known issues. It also incorporates all fixes made in version 2018.7 and earlier, which you can find described in the Release notes.

Fixes where mdrun could behave incorrectly

Fix missing interactions with domain decomposition

When running with domain decomposition, any interactions described by the rarely-used topology file section [ intermolecular_interactions ] were ignored. This did not affect normal non-bonded or intra-molecular interactions.

Issue 2953

Fix possible floating point exception during minimization.

It was possible that very small forces during minimization could lead to a crash due to a divide by zero error. Fixed by introducing a check.

Issue 2917

Fix segmentation fault when using membrane embedding

Issue 2947

Allow AWH with pull-geometry ‘direction’ to be periodic

When applying AWH to a pull coordinate with geometry ‘direction’ with a AWH interval length of more than 95% of the box size, the dimension is now made periodic.

Issue 2946

Fixes for gmx tools

Fixed residue and molecule indexing in selections

Issue 2951

Fix PQR formatting

The formatting was incorrect for some tools that use PQR files.

Issue 2955

Fix gmx wham with angle geometries

gmx wham would mix up degree and radian units leading to no overlap or not-a-number output. Note: this fix is not correct, a correct fix is applied in the next patch release.

Issue 2609 Issue 3094

Add some information for grompp error with wrong line endings

Give meaningful error with too large grid in hbond

When using a grid that is too large hbond could try to allocate enough memory to cause a crash.

Issue 2962

Add some information for syntax errors with include delimiters in grompp

Issue 2911

Fixes that affect portability

Fixed wider reference SIMD setups

The reference SIMD builds could use a too small memory alignment, leading to mdrun exiting with an alignment error

Issue 2952

Fixed build failure with Apple Clang

Builds would fail because of qsort being undefined.


Removed non-existent mdp option awh1-dim1-period from user guide

Issue 2940

Add checks for too many interactions during memory allocation

Issue 2932