Bugs fixed#

Verlet buffer set correctly for inhomogeneous systems#

The Verlet buffer estimation now uses an effective density for the system computing from the initial coordinates. This avoids underestimation of the buffer for (very) inhomogeneous systems.

Issue 4509

Fix segmentation fault for large atom and thread count#

When the number of atoms times the number of OpenMP threads was larger than 2147483647, negative atom number could cause illegal memory access.

Issue 4628

Density-guided simulation normalization#

With the .mdp option density-guided-simulation-normalize-densities = yes , the reference density and the simulated density values were previously divided by the sum of their values.

This lead to surprising behavior for reference densities with lots of negative voxel values: the density started to “repel” the protein structure instead of attracting it, if the total sum of voxel values was smaller than zero. The negative normalization constant lead to a sign change in voxel values.

To avoid this behavior, the reference density is now normalized so that the sum of positive values is unity, ensuring that the normalization constant is always positive.

Apart from avoiding the unexpected behavior, we expect that this also leads to smaller absolute differences between reference density and simulated density, with some small benefits for numerical stability.

This change affects all simulations where voxel values are negative (usually this excludes synthetic data) and that are run with density-guided-simulation-normalize-densities = yes, but only has a larger effect for: first, similarity measure inner-product as an effective force-constant scaling and, second, for all similarity measures where the sum of all voxel values was negative.

gmxapi Python package avoids unnecessary MPI initialization#

Delayed initialization of MPI (due to automatic behavior of mpi4py) avoids MPI initialization that previously occurred just by importing gmxapi. The previous behavior has been seen to cause strange interactions with resource management libraries like libfabric at unexpected times (such as during package installation) with gmxapi version 0.3.

Issue 4693

Fail-safe check for perturbed exclusions beyond rlist#

With free-energy calculations, excluded non-bonded interactions involving at least one perturbed atom should not be beyond rlist when using PME. The check for this could have false negatives. Now the check is fail safe and will always trigger a fatal error when perturbed excluded pairs are beyond rlist.

Issue 3403 Issue 4321 Issue 4461