GROMACS 2021.4 release notes

This version was released on November 5th, 2021. These release notes document the changes that have taken place in GROMACS since the previous 2021.3 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

Fixed crash for large system with virtual sites

When large system with virtual sites were ran with domain decomposition and OpenMP threading, mdrun would crash when the number of atoms in a domain and its halo were more than 200000.

Issue 4167

Fixed bug with GPU LINCS occasionally shifting atoms in wrong direction

Due to missing blocking synchronizations in the CUDA version of LINCS, the shared memory was occasionally overwritten with the new data. This may slightly affect the final coordinates of the shifted atoms.

Issue 4199

Disabled the use of PME Mixed mode for FEP simulations

The use of Mixed mode PME (-pme gpu -pmefft cpu) led to incorrect computation of \({\frac{\partial V}{\partial {\lambda}}}\) in FEP simulations.

Mixed mode is only used when explicitly requested by the user.

Issue 4190

Fixed spurious nan in AWH free energy output when running FEP with other dimensions

When running AWH with alchemical free energy perturbations as one of multiple dimensions the free energy output could contain nan entries due to failing log operations. This did not affect the AWH bias, which means that the simulations were not affected as such, but the output was.

Issue 4180

Made mdrun work without MPI

When configured with neither of MPI or thread-MPI, mdrun would terminate with an assertion failure.

Issue 4264

Fixes for gmx tools

Fix gmx convert-tpr -s -o

Formerly, this combination could be used when supplying an index file. Now this combination can also be used with default index groups when not supplying an index file.

grompp now prints a note again when combining center of mass motion removal and position restraints

Issue 4128

Static selections of large index groups now work

Commands like gmx distance -f traj.xtc -n ndx.ndx -select "group \"Contacts\"" only worked if the size of Contacts was less than the number of atoms. This restriction was a bug, and has been fixed so that Contacts make take any size.

Other similar uses of static selections derived from index groups will also now work.

Issue 4148

Static selections of index groups with repeated indices now work

Static groups from index files referenced in selections (e.g. gmx tool -select "group \"Contacts\"") only worked correctly if they never had adjacent repeats of the same index within the group. Repeating the same index can be meaningful e.g. in lists of inter-atomic distances to analyze with gmx distance to analyze "1 2 2 3". Previously, the index group had to be written like "2 3 1 2" in order to work.

Issue 4149

Fixes that affect portability


Fix a bug affecting re-run gmxapi scripts

A typo may have prevented gmxapi simulations from continuing from checkpoints after being interrupted. Fixed in version 0.2.3 of the gmxapi Python package.

Issue 4267