# Segmentation Fault, Error during \`gmx grompp\` **URL:** https://gromacs.bioexcel.eu/t/segmentation-fault-error-during-gmx-grompp/9574 **Category:** User discussions **Tags:** mdp-parameters, grompp, mdrun **Created:** [July 4, 2024, 2:40pm UTC](https://gromacs.bioexcel.eu/t/segmentation-fault-error-during-gmx-grompp/9574 "2024-07-04T14:40:46Z") **Posts on this page:** 2 **Page:** 1
### Author: ![kinetico](https://avatars.discourse-cdn.com/v4/letter/k/9de053/32.png) [@kinetico](https://gromacs.bioexcel.eu/u/kinetico) #### Post date: [July 4, 2024, 2:40pm UTC](https://gromacs.bioexcel.eu/t/segmentation-fault-error-during-gmx-grompp/9574/1 "2024-07-04T14:40:46Z")
GROMACS version: 2023 GROMACS modification: No Hello everyone, I am encountering a segmentation fault error while running `gmx grompp`. Here are the details of my setup and the error messages I am receiving: **Commands Executed** 1. Preparation of the `.tpr` file: gmx grompp -f nvt.mdp -c gromacs.gro -o gromacs\_try.tpr -n index.ndx -p gromacs.top -maxwarn 5 **Error Messages** During the execution of `gmx mdrun`, I receive the following error: ``` :-) GROMACS - gmx grompp, 2023 (-: ``` Executable: /usr/local/gromacs/bin/gmx Data prefix: /usr/local/gromacs Command line: gmx grompp -f nvt.mdp -c gromacs.gro -o gromacs\_try.tpr -n index.ndx -p gromacs.top -maxwarn 5 Setting the LD random seed to 1875893429 Generated 1275 of the 1275 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 1275 of the 1275 1-4 parameter combinations Excluding 3 bonded neighbours molecule type ‘system1’ turning H bonds into constraints… Excluding 3 bonded neighbours molecule type ‘72Y’ turning H bonds into constraints… Excluding 3 bonded neighbours molecule type ‘Na+’ turning H bonds into constraints… Excluding 3 bonded neighbours molecule type ‘Cl-’ turning H bonds into constraints… Excluding 3 bonded neighbours molecule type ‘Na+’ Excluding 3 bonded neighbours molecule type ‘Cl-’ Excluding 3 bonded neighbours molecule type ‘Na+’ Excluding 3 bonded neighbours molecule type ‘Cl-’ Excluding 3 bonded neighbours molecule type ‘Na+’ Excluding 3 bonded neighbours molecule type ‘Cl-’ Excluding 3 bonded neighbours molecule type ‘Na+’ Excluding 3 bonded neighbours molecule type ‘Cl-’ Excluding 3 bonded neighbours molecule type ‘Na+’ Excluding 3 bonded neighbours molecule type ‘Cl-’ Excluding 3 bonded neighbours molecule type ‘Na+’ Excluding 3 bonded neighbours molecule type ‘Cl-’ Excluding 3 bonded neighbours molecule type ‘Na+’ Excluding 3 bonded neighbours molecule type ‘Cl-’ Excluding 3 bonded neighbours molecule type ‘Na+’ Excluding 3 bonded neighbours molecule type ‘Cl-’ Excluding 3 bonded neighbours molecule type ‘Na+’ Excluding 3 bonded neighbours molecule type ‘Cl-’ Excluding 3 bonded neighbours molecule type ‘Na+’ Excluding 3 bonded neighbours molecule type ‘Cl-’ Excluding 3 bonded neighbours molecule type ‘Na+’ Excluding 3 bonded neighbours molecule type ‘Cl-’ Excluding 3 bonded neighbours molecule type ‘Na+’ Excluding 3 bonded neighbours molecule type ‘Cl-’ Excluding 3 bonded neighbours molecule type ‘Na+’ Excluding 3 bonded neighbours molecule type ‘Cl-’ Excluding 3 bonded neighbours molecule type ‘Na+’ Excluding 3 bonded neighbours molecule type ‘Cl-’ Excluding 3 bonded neighbours molecule type ‘Na+’ Excluding 3 bonded neighbours molecule type ‘Cl-’ Excluding 3 bonded neighbours molecule type ‘Na+’ Excluding 3 bonded neighbours molecule type ‘Cl-’ Excluding 3 bonded neighbours molecule type ‘Na+’ Excluding 3 bonded neighbours molecule type ‘Cl-’ Excluding 3 bonded neighbours molecule type ‘Na+’ Excluding 3 bonded neighbours molecule type ‘Cl-’ Excluding 3 bonded neighbours molecule type ‘Na+’ Excluding 3 bonded neighbours molecule type ‘Cl-’ Excluding 3 bonded neighbours molecule type ‘Na+’ Excluding 3 bonded neighbours molecule type ‘Cl-’ Excluding 3 bonded neighbours molecule type ‘Na+’ Excluding 3 bonded neighbours molecule type ‘Cl-’ Excluding 3 bonded neighbours molecule type ‘Na+’ Excluding 3 bonded neighbours molecule type ‘Cl-’ Excluding 3 bonded neighbours molecule type ‘Na+’ Excluding 3 bonded neighbours molecule type ‘Cl-’ Excluding 3 bonded neighbours molecule type ‘Na+’ Excluding 3 bonded neighbours molecule type ‘Cl-’ Excluding 3 bonded neighbours molecule type ‘Na+’ Excluding 3 bonded neighbours molecule type ‘Cl-’ Excluding 3 bonded neighbours molecule type ‘Na+’ Excluding 3 bonded neighbours molecule type ‘Cl-’ Excluding 3 bonded neighbours molecule type ‘Na+’ Excluding 3 bonded neighbours molecule type ‘Cl-’ Excluding 3 bonded neighbours molecule type ‘Na+’ Excluding 3 bonded neighbours molecule type ‘Cl-’ Excluding 3 bonded neighbours molecule type ‘Na+’ Excluding 3 bonded neighbours molecule type ‘Cl-’ Excluding 3 bonded neighbours molecule type ‘Na+’ Excluding 3 bonded neighbours molecule type ‘Cl-’ Excluding 3 bonded neighbours molecule type ‘Na+’ Excluding 3 bonded neighbours molecule type ‘Cl-’ Excluding 3 bonded neighbours molecule type ‘Na+’ Excluding 3 bonded neighbours molecule type ‘Cl-’ Excluding 3 bonded neighbours molecule type ‘Na+’ Excluding 3 bonded neighbours molecule type ‘WAT’ turning H bonds into constraints… NOTE 1 [file gromacs.top, line 36940]: System has non-zero total charge: 0.004001 Total charge should normally be an integer. See http:/www.gromacs.org/Documentation/Floating\_Point\_Arithmetic for discussion on how close it should be to an integer. WARNING 1 [file gromacs.top, line 36940]: You are using Ewald electrostatics in a system with net charge. This can lead to severe artifacts, such as ions moving into regions with low dielectric, due to the uniform background charge. We suggest to neutralize your system with counter ions, possibly in combination with a physiological salt concentration. ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ J. S. Hub, B. L. de Groot, H. Grubmueller, G. Groenhof Quantifying Artifacts in Ewald Simulations of Inhomogeneous Systems with a Net Charge J. Chem. Theory Comput. 10 (2014) pp. 381-393 -------- -------- — Thank You — -------- -------- Setting gen\_seed to -457179185 Velocities were taken from a Maxwell distribution at 300 K Cleaning up constraints and constant bonded interactions with virtual sites Number of degrees of freedom in T-Coupling group Protein\_72Y is 8278.72 Number of degrees of freedom in T-Coupling group Water\_Na+\_Cl- is 79014.28 The largest distance between excluded atoms is 0.427 nm between atom 22 and 30 Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K Segmentation fault (core dumped) **Attached files** 1. nvt.mdp [nvt.mdp](https://gromacs.bioexcel.eu/uploads/short-url/wnCHcqWscHqlwirgRoxgjQFTejC.mdp) (6.5 KB) 2. gromacs.top [gromacs.top](https://gromacs.bioexcel.eu/uploads/short-url/tTV398xQhJxUVoVvxawBpUVjYdL.top) (1.8 MB) If you need I can also share the file gromacs.gro and index.ndx **Request for Help** Has anyone encountered similar issues or have suggestions on how to resolve this problem? Any advice would be greatly appreciated! Thank you in advance for your help! Antonio ---
### Author: ![MagnusL](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/magnusl/32/2380_2.png) [@MagnusL](https://gromacs.bioexcel.eu/u/MagnusL) #### Post date: [July 5, 2024, 6:39am UTC](https://gromacs.bioexcel.eu/t/segmentation-fault-error-during-gmx-grompp/9574/2 "2024-07-05T06:39:03Z")
It looks very similar to [grompp crashes in computeEffectiveAtomDensity (#5002) · Issues · GROMACS / GROMACS · GitLab](https://gitlab.com/gromacs/gromacs/-/issues/5002). In that case it has been fixed in the 2023.5 release.