GROMACS 2021.6 release notes

This version was released on July 8th, 2022. These release notes document the changes that have taken place in GROMACS since the previous 2021.5 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

Extend error message for free-energy exclusion beyond rlist

With free-energy decoupling simulations an error for exclusions beyond rlist can occur due to a too small box. This cause is now added to the error message.

Issue 3403 Issue 3808

Fix running with LJ PME only

Simulations with only LJ PME but not electrostatic PME would fail to run due to an error in task assignment.

Issue 4362

Fix missing synchronization in CUDA update kernels

When using GPU update with SETTLE or LINCS constraints, virial calculations could have been incorrect on Volta and newer NVIDIA GPUs, which in turn would lead to incorrect pressure. The GPU update is not enabled by default, so the error can only appear in simulations where it was manually selected, and even in this case the error might be rare since we have not observed it in practice in the testing we have performed.

To check whether your runs could have been affected, please examine your mdrun log file:

  • Look for the line “GPU support: CUDA”;
  • Look for the line “PP task will update and constrain coordinates on the GPU”;
  • Check whether any GPU the value of “compute cap.” 7.0 or higher in the “GPU Info:” section.

If all three are present, than the bug could have perturbed the virial calculation and, in turn, led to incorrect pressure coupling. All GROMACS version prior to 2021.6 and 2022.0 that allow offloading of the update and constraint calculations to GPUs are affected.

Issue 4393

Fixes for gmx tools

Do not try to guess atom names in gmx rms unless needed

Guessing atomic masses based on atom names may sometimes fail. When -nomw switch is used, atom masses are not needed, but gmx rms was trying to guess them anyway, throwing a fatal error when an unknown element was encountered. Now, the error is only raised when masses are actually needed.

Issue 4356

Fixes that affect portability


Corrects units for AWH interval in the user guide

When applying AWH to angles or dihedrals, the units of bonds of the sampling interval listed in the mdp section of the user guide are now stated to be in degrees. The guide incorrectly stated that there were in radians, whereas the code interprets the user input as degrees.

Issue 4367

Fix distance restraint force calculation in case of negative prefactor

When calculating distance restraint forces, the quadratic regime for weak restraint violation and the linear regime for strong restraint violation were interchanged in case of a negative force constant.

Issue 4347