## Summary When an atom is outside the box, [index calculation in `computeEffectiveAtomDensity`](https://gitlab.com/gromacs/gromacs/blob/71d0092693a303ac5633b2d458f1602217139a6b/src/gromacs/mdlib/calc_verletbuf.cpp#L1133) produces negative values, and GROMACS crashes due to heap corruption. Specifically, the problem seems to be caused by negative coordinates (-8.229) of magnitude larger than the box size (6.2), so that our `+ numCells[d]` is not enough to make the value positive. ## Unit test For `src/gromacs/mdlib/tests/calc_verletbuf.cpp`: ```cpp // Issue #5002 TEST(EffectiveAtomDensity, LargeValuesHandledWell) { const std::vector<RVec> coordinates = { { 13.132, -8.229, -2.700 } }; const matrix box = { { 6.2, 0, 0 }, { 0, 6.2, 0 }, { 0, 0, 6.2 } }; const real cutoff = 1; const real referenceDensity = (1) / (coordinates.size() * gmx::power3<real>(6.2/6)); const real density = computeEffectiveAtomDensity(coordinates, box, cutoff, MPI_COMM_NULL); EXPECT_FLOAT_EQ(density, referenceDensity); } ``` ## Exact steps to reproduce Reproducible with current 2024 and 2023 versions: [run.mdp](/uploads/c6ae2a38f0050ad028c6a222349e9f4a/run.mdp) [system.gro](/uploads/9260751be60b51694877c5f5d320f08e/system.gro) [system.top](/uploads/61625de074afe4369a2614d3ef5bb3aa/system.top) ```console $ ~/gromacs-2023/build/clang-17/bin/gmx grompp -f run.mdp -c system.gro -p system.top -o run.tpr :-) GROMACS - gmx grompp, 2023.5-dev-20240219-db90c39977 (-: Executable: /home/aland/gromacs-2023/build/clang-17/bin/gmx Data prefix: /home/aland/gromacs-2023 (source tree) Working dir: /home/aland/issue-f8399 Command line: gmx grompp -f run.mdp -c system.gro -p system.top -o run.tpr NOTE 1 [file run.mdp]: For a correct single-point energy evaluation with nsteps = 0, use continuation = yes to avoid constraining the input coordinates. WARNING 1 [file run.mdp]: The Berendsen thermostat does not generate the correct kinetic energy distribution, and should not be used for new production simulations (in our opinion). We would recommend the V-rescale thermostat. Setting the LD random seed to -1120502286 Generated 1 of the 1 non-bonded parameter combinations Excluding 3 bonded neighbours molecule type 'molecule' Analysing residue names: There are: 1 Other residues Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... Number of degrees of freedom in T-Coupling group System is 0.00 Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K munmap_chunk(): invalid pointer Aborted (core dumped) ``` Original report: https://gromacs.bioexcel.eu/t/gmx-grompp-crashes-with-a-very-simple-system/8399/1