GROMACS 2021.2 release notes

This version was released on May 5th, 2021. These release notes document the changes that have taken place in GROMACS since the previous 2021.1 version, to fix known issues. It also incorporates all fixes made in version 2020.6 and earlier, which you can find described in the Release notes.

Fixes where mdrun could behave incorrectly

Removed a potential race condition with GPU update

Fixed possible (but so far unobserved) race condition in coordinate copy when using GPU update with dipole moment calculation.

Issue 4024

Avoided issues with global reduction observed with md-vv

The new implementation for md-vv in the modular simulator could produce floating-point exceptions computing values on non-master ranks that were never used. This is now fixed by avoiding that computation. The other integrators were unaffected because they over-wrote the values computed.

Issue 4031

Prohibited SETTLE interactions for atoms with perturbed masses

Older implementations produced varying degrees of wrong results because this has never been implemented. Now both mdrun and grompp refuse to handle such a system, suggesting using normal constraints.

Issue 3959

Rerun now writes pull output correctly

Refactoring omitted to preserve that pullf.xvg and pullx.xvg files should be written during a rerun. All 2019 and 2020 versions were affected, as well as 2021 and 2021.1. The pull output files are now written as they used to be in 2018 and earlier.

Issue 4043

Fixes for gmx tools

Fix incorrect behaviour with single residue chains in pdb2gmx

The code for chcking for cyclic molecules could lead to single residue chains incorrectly to be assigned as circular molecules.

Issue 4029

Fix grompp check for position restraints with absolute reference

Fixed that grompp with position restraints would always issue a warning about using an absolute reference, even when an absolute reference was not used.

Issue 3996

Fix error when using VMD plugin

Tools would crash with a C++ library assertion because the plugin loading code incorrectly tried to construct a string from nullptr.

Issue 3055

Fix file permissions with gmx solvate and gmx genion

These used to write temporary files with Unix permissions 0600. Now they respect the umask of the process (typically 0644).

Issue 4040

Fixes that affect portability

Support for Intel oneAPI compiler 2021.2

Fixed compiler infinity math and MKL flags.

Fix Apple OpenCL build

Issue 4008

Fixed compilation issue with GCC 11

Issue 4039


Fix bond type in GROMOS force fields

The bond type for C and +N in [ACE] was incorrect.

Issue 3995

Allow PME on CPU in runs with domain decomposition and GPU update

Relaxed a limitation which prevented running parallel runs with domain decomposition and GPU update to use the CPU for PME (as long as combined PP-PME ranks are used). This allows parallel runs to scale when the CPU resources are sufficient for PME.

Issue 4035