# \#mdrun-crash **URL:** https://gromacs.bioexcel.eu/tag/mdrun-crash/30.md [Latest](https://gromacs.bioexcel.eu/latest.md) · [Categories](https://gromacs.bioexcel.eu/categories.md) · [Tags](https://gromacs.bioexcel.eu/tags.md) --- ## [CUDA illegal memory access during NPT equilibration](https://gromacs.bioexcel.eu/t/cuda-illegal-memory-access-during-npt-equilibration/13673)
**Author:** [@shreyasd2](https://gromacs.bioexcel.eu/u/shreyasd2)\ **Replies:** 9\ **Last updated:** [August 21, 2026, 4:08pm UTC](https://gromacs.bioexcel.eu/t/cuda-illegal-memory-access-during-npt-equilibration/13673 "2026-08-21T16:08:51Z")
GROMACS version: 2026.0 GROMACS modification: No Dear all, I am simulating a highly dense system containing carbohydrates and amino acids. I am performing a multistep equilibration protocol with gradually decreasing f… --- ## [LINCS Error in production run](https://gromacs.bioexcel.eu/t/lincs-error-in-production-run/10434)
**Author:** [@athiras](https://gromacs.bioexcel.eu/u/athiras)\ **Replies:** 2\ **Last updated:** [May 1, 2026, 10:45am UTC](https://gromacs.bioexcel.eu/t/lincs-error-in-production-run/10434 "2026-05-01T10:45:24Z")
GROMACS version: 2021.1 GROMACS modification: Yes/No Here post your question I am currently running a 1 ns production molecular dynamics (MD) simulation with restraints, but I’m encountering persistent LINCS warnings … --- ## [Unusal barostat instability when using rocm-heffte that is not present when using vkfft](https://gromacs.bioexcel.eu/t/unusal-barostat-instability-when-using-rocm-heffte-that-is-not-present-when-using-vkfft/13045)
**Author:** [@mick](https://gromacs.bioexcel.eu/u/mick)\ **Replies:** 1\ **Last updated:** [December 16, 2025, 5:05pm UTC](https://gromacs.bioexcel.eu/t/unusal-barostat-instability-when-using-rocm-heffte-that-is-not-present-when-using-vkfft/13045 "2025-12-16T17:05:30Z")
GROMACS version: 2025.4 GROMACS modification: Yes: AdaptiveCPP 25.04 w/HeFFTe MPICH 3.1.32, rocm/6.4.2 & LLVM19 Hello folks, I have been trying to run a fairly large (12M atom) system with anisotopic pressure coupling… --- ## [Segmentation fault error in mdrun](https://gromacs.bioexcel.eu/t/segmentation-fault-error-in-mdrun/11660)
**Author:** [@roozi](https://gromacs.bioexcel.eu/u/roozi)\ **Replies:** 4\ **Last updated:** [March 5, 2025, 11:09am UTC](https://gromacs.bioexcel.eu/t/segmentation-fault-error-in-mdrun/11660 "2025-03-05T11:09:57Z")
GROMACS version:2024.3 GROMACS modification: No Hi. When I run an awh simulation of a protein solution on gromacs 2024.3 I get segmentation fault (core dumped) upon starting the simulation. I do not think it is due to… --- ## [Mdrun not starting on Windows 10](https://gromacs.bioexcel.eu/t/mdrun-not-starting-on-windows-10/10583)
**Author:** [@Elenna](https://gromacs.bioexcel.eu/u/Elenna)\ **Replies:** 0\ **Last updated:** [November 19, 2024, 8:59am UTC](https://gromacs.bioexcel.eu/t/mdrun-not-starting-on-windows-10/10583 "2024-11-19T08:59:12Z")
GROMACS version: 2024.4 GROMACS modification: No Greeting everyone. I am still pretty new to GROMACS. Currently, I have an issue with mdrun on my installed GROMACS on windows. The terminal is unable to recognize mdru… --- ## [No reference data for first slab (n=-2147483648) while using enforced rotation](https://gromacs.bioexcel.eu/t/no-reference-data-for-first-slab-n-2147483648-while-using-enforced-rotation/7376)
**Author:** [@jpkrowe](https://gromacs.bioexcel.eu/u/jpkrowe)\ **Replies:** 3\ **Last updated:** [June 26, 2024, 11:48am UTC](https://gromacs.bioexcel.eu/t/no-reference-data-for-first-slab-n-2147483648-while-using-enforced-rotation/7376 "2024-06-26T11:48:00Z")
GROMACS version:2021.5 GROMACS modification: Yes - patched with plumed-2.8.0 Dear All, I am running a metadynamics simulation with plumed, whilst using enforced rotation to stop my molecule from rotating. After around… --- ## [MDRUN crash during gREST simulation under NVT ensemble](https://gromacs.bioexcel.eu/t/mdrun-crash-during-grest-simulation-under-nvt-ensemble/6535)
**Author:** [@jimmy\_chang](https://gromacs.bioexcel.eu/u/jimmy_chang)\ **Replies:** 1\ **Last updated:** [June 26, 2023, 4:21pm UTC](https://gromacs.bioexcel.eu/t/mdrun-crash-during-grest-simulation-under-nvt-ensemble/6535 "2023-06-26T16:21:29Z")
GROMACS version: 2022.3 GROMACS modification: No Hello everyone. I am currently using GROMACS ver. 2022.3 patched with PLUMED ver. 2.8.1., and I’ve been trying to replicate the gREST simulations from Oshima et al. (J.… --- ## [Mdrun Instability with deprotonated ARG topology with CHARMM36](https://gromacs.bioexcel.eu/t/mdrun-instability-with-deprotonated-arg-topology-with-charmm36/5554)
**Author:** [@cordesm](https://gromacs.bioexcel.eu/u/cordesm)\ **Replies:** 0\ **Last updated:** [January 12, 2023, 12:40am UTC](https://gromacs.bioexcel.eu/t/mdrun-instability-with-deprotonated-arg-topology-with-charmm36/5554 "2023-01-12T00:40:55Z")
GROMACS version: 2022.4 GROMACS modification: No When altering the protonation state of a positively charged ARG to a neutral ARGN using topologies from pdb2gmx with the -arg flag enabled with the charmm36 FF, there se… --- ## [System blowing up in decoupled ligand (in protein complex) simulation for ABFE calculations](https://gromacs.bioexcel.eu/t/system-blowing-up-in-decoupled-ligand-in-protein-complex-simulation-for-abfe-calculations/4891)
**Author:** [@abvel](https://gromacs.bioexcel.eu/u/abvel)\ **Replies:** 9\ **Last updated:** [October 11, 2022, 5:05pm UTC](https://gromacs.bioexcel.eu/t/system-blowing-up-in-decoupled-ligand-in-protein-complex-simulation-for-abfe-calculations/4891 "2022-10-11T17:05:03Z")
GROMACS version: 2019.2 GROMACS modification: No Hi everybody, For the past couple of months I’ve been trying to use Gromacs to calculate the Absolute Binding Free Energy (ABFE) of a ligand to a protein-RNA complex vi… --- ## [Fatal error: Setting the number of thread-MPI ranks is only supported with thread-MPI and GRO](https://gromacs.bioexcel.eu/t/fatal-error-setting-the-number-of-thread-mpi-ranks-is-only-supported-with-thread-mpi-and-gro/4488)
**Author:** [@Fabiano](https://gromacs.bioexcel.eu/u/Fabiano)\ **Replies:** 0\ **Last updated:** [July 22, 2022, 1:33am UTC](https://gromacs.bioexcel.eu/t/fatal-error-setting-the-number-of-thread-mpi-ranks-is-only-supported-with-thread-mpi-and-gro/4488 "2022-07-22T01:33:41Z")
GROMACS version: 2021.4 GROMACS modification: No Hello everyone! I am trying to parallelize some testings to learn using efficiently gromacs in a cluster. By using a small amount of resources via SLURM schedule (i.e.… --- ## [Issue with segmentation fault](https://gromacs.bioexcel.eu/t/issue-with-segmentation-fault/3669)
**Author:** [@Vidya](https://gromacs.bioexcel.eu/u/Vidya)\ **Replies:** 0\ **Last updated:** [February 15, 2022, 6:10am UTC](https://gromacs.bioexcel.eu/t/issue-with-segmentation-fault/3669 "2022-02-15T06:10:11Z")
GROMACS version: 2021.2, 2019.6 GROMACS modification: Yes Here post your question I am facing a segmentation fault issue with GROMACS patched with plumed and I was wondering if you could help me. I am trying to run a … --- ## [Error: X particles communicated to PME rank N](https://gromacs.bioexcel.eu/t/error-x-particles-communicated-to-pme-rank-n/3114)
**Author:** [@David\_SB](https://gromacs.bioexcel.eu/u/David_SB)\ **Replies:** 1\ **Last updated:** [November 16, 2021, 11:24am UTC](https://gromacs.bioexcel.eu/t/error-x-particles-communicated-to-pme-rank-n/3114 "2021-11-16T11:24:06Z")
GROMACS version: 2020 GROMACS modification: No Dear all, I’m currently trying to extend my simulations of a peptide from a checkpoint by using mpirun gmx\_mpi mdrun and I’m getting the following error: 22 particles co… --- ## [Continuing simulation with cpt file after a crash](https://gromacs.bioexcel.eu/t/continuing-simulation-with-cpt-file-after-a-crash/2200)
**Author:** [@struc\_bio](https://gromacs.bioexcel.eu/u/struc_bio)\ **Replies:** 2\ **Last updated:** [June 26, 2021, 9:49am UTC](https://gromacs.bioexcel.eu/t/continuing-simulation-with-cpt-file-after-a-crash/2200 "2021-06-26T09:49:23Z")
GROMACS modification: No Can we continue a simulation using -cpi .cpt file after it has written a series of step.pdb files and crashed in previous step (after ~800 ns)? Can I simply resubmit the mdrun command with cpt … --- ## [Error after restarting: particles communicated to PME rank 0 are more than 2/3 times the cut-off](https://gromacs.bioexcel.eu/t/error-after-restarting-particles-communicated-to-pme-rank-0-are-more-than-2-3-times-the-cut-off/2231)
**Author:** [@rcrehuet](https://gromacs.bioexcel.eu/u/rcrehuet)\ **Replies:** 0\ **Last updated:** [May 27, 2021, 10:46am UTC](https://gromacs.bioexcel.eu/t/error-after-restarting-particles-communicated-to-pme-rank-0-are-more-than-2-3-times-the-cut-off/2231 "2021-05-27T10:46:47Z")
GROMACS version: 2019.4 GROMACS modification: with plumed Dear all, My simulation has crashed with the following error: ------------------------------------------------------- Program: gmx mdrun, version 2019.4 S…