# Segmentation fault (core dumped) **URL:** \ **Category:** User discussions\ **Created:** [June 30, 2020, 12:01pm UTC](https://gromacs.bioexcel.eu/t/segmentation-fault-core-dumped/402 "2020-06-30T12:01:32Z")\ **Posts on this page:** 9\ **Page:** 1
**Author:** ![veerubiotech](https://avatars.discourse-cdn.com/v4/letter/v/e480ec/32.png) [@veerubiotech](https://gromacs.bioexcel.eu/u/veerubiotech)\ **Post date:** [June 30, 2020, 12:01pm UTC](https://gromacs.bioexcel.eu/t/segmentation-fault-core-dumped/402/1 "2020-06-30T12:01:32Z")
GROMACS version: 2020.2 GROMACS modification: Yes/No Here post your question Dear All, I am new to MD simulation. I just installed gromacs on my dell G5 5590 laptop. i was going through tutorial Membrane Protein: KALP15 in DPPC. I got the following error when i run - gmx genrestr -f KALP\_newbox.gro -o strong\_posre.itp -fc 100000 100000 100000 GROMACS: gmx genrestr, version 2020.2 Executable: /usr/local/gromacs/bin/gmx Data prefix: /usr/local/gromacs Working dir: /mnt/c/Users/veeru/Dropbox/Amity/CoronaVirus/S-Protein/S2/MDS/tut Command line: gmx genrestr -f KALP\_newbox.gro -o strong\_posre.itp -fc 100000 100000 100000 Reading structure file Select group to position restrain Segmentation fault (core dumped) May i know how to solve this? Thank you Best Regards Veeru ---
**Author:** ![jalemkul](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/jalemkul/32/18_2.png) [@jalemkul](https://gromacs.bioexcel.eu/u/jalemkul)\ **Post date:** [July 1, 2020, 3:47pm UTC](https://gromacs.bioexcel.eu/t/segmentation-fault-core-dumped/402/2 "2020-07-01T15:47:22Z")
This is a bug. Please open an issue on [gitlab.com/gromacs](http://gitlab.com/gromacs) ---
**Author:** ![keeperw](https://avatars.discourse-cdn.com/v4/letter/k/439d5e/32.png) [@keeperw](https://gromacs.bioexcel.eu/u/keeperw)\ **Post date:** [August 2, 2020, 10:14am UTC](https://gromacs.bioexcel.eu/t/segmentation-fault-core-dumped/402/3 "2020-08-02T10:14:44Z")
Thank you for the reply of jalemkul. I faced the exactly same problem. Can you explan more? with great thanks. ---
**Author:** ![jalemkul](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/jalemkul/32/18_2.png) [@jalemkul](https://gromacs.bioexcel.eu/u/jalemkul)\ **Post date:** [August 2, 2020, 10:27am UTC](https://gromacs.bioexcel.eu/t/segmentation-fault-core-dumped/402/4 "2020-08-02T10:27:38Z")
It has already been fixed. Install version 2020.3 and try again. ---
**Author:** ![keeperw](https://avatars.discourse-cdn.com/v4/letter/k/439d5e/32.png) [@keeperw](https://gromacs.bioexcel.eu/u/keeperw)\ **Post date:** [August 5, 2020, 7:52am UTC](https://gromacs.bioexcel.eu/t/segmentation-fault-core-dumped/402/5 "2020-08-05T07:52:33Z")
It worked! Thank you very much. ---
**Author:** ![Kaff](https://avatars.discourse-cdn.com/v4/letter/k/f19dbf/32.png) [@Kaff](https://gromacs.bioexcel.eu/u/Kaff)\ **Post date:** [August 30, 2020, 3:20am UTC](https://gromacs.bioexcel.eu/t/segmentation-fault-core-dumped/402/6 "2020-08-30T03:20:38Z")
Disculpe la molestia, yo también soy nueva en el tema y lo que entendí es que hay que actualizar la versión de Gromacs a la 2020.3? Gracias. ---
**Author:** ![jalemkul](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/jalemkul/32/18_2.png) [@jalemkul](https://gromacs.bioexcel.eu/u/jalemkul)\ **Post date:** [August 30, 2020, 11:52am UTC](https://gromacs.bioexcel.eu/t/segmentation-fault-core-dumped/402/7 "2020-08-30T11:52:22Z")
@Kaff please compose your posts in English. ---
**Author:** ![espiral17](https://avatars.discourse-cdn.com/v4/letter/e/ce73a5/32.png) [@espiral17](https://gromacs.bioexcel.eu/u/espiral17)\ **Post date:** [October 1, 2020, 3:23pm UTC](https://gromacs.bioexcel.eu/t/segmentation-fault-core-dumped/402/8 "2020-10-01T15:23:02Z")
I have installed GROMACS 2020.1, and I have experienced the same problem with this command gmx genrestr -f KALP\_newbox.gro -o strong\_posre.itp -fc 100000 100000 100000 “Reading structure file Select group to position restrain Segmentation fault (core dumped)” Thus, I am going to upgrade to the 2020.3 version. And I would like to know this: How is possible to get GPU enabled? it seems to be impossible in my workstation which it has an ASUS C621e motherboard with two intel xeon gold 6138 processors, 96 gb in RAM in addition to two GPU GeForce RTX cards (2080Ti), compatible with GPU acceleration for GROMACS ---
**Author:** ![ruhul](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/ruhul/32/2014_2.png) [@ruhul](https://gromacs.bioexcel.eu/u/ruhul)\ **Post date:** [May 1, 2023, 3:20am UTC](https://gromacs.bioexcel.eu/t/segmentation-fault-core-dumped/402/9 "2023-05-01T03:20:39Z")
During the energy minimization step, I faced the error, Segmentation fault (core dumped). ruhul@ruhul:~/Documents/glucosidase\_acarbose$ gmx grompp -f em.mdp -c complex\_solv\_ions.gro -p topol.top -o em.tpr :-) GROMACS - gmx grompp, 2021.4-Ubuntu-2021.4-2 (-: ``` GROMACS is written by: Andrey Alekseenko Emile Apol Rossen Apostolov Paul Bauer Herman J.C. Berendsen Par Bjelkmar Christian Blau Viacheslav Bolnykh Kevin Boyd Aldert van Buuren Rudi van Drunen Anton Feenstra Gilles Gouaillardet Alan Gray Gerrit Groenhof Anca Hamuraru Vincent Hindriksen M. Eric Irrgang Aleksei Iupinov Christoph Junghans Joe Jordan Dimitrios Karkoulis Peter Kasson Jiri Kraus Carsten Kutzner Per Larsson Justin A. Lemkul Viveca Lindahl Magnus Lundborg Erik Marklund Pascal Merz Pieter Meulenhoff Teemu Murtola Szilard Pall Sander Pronk Roland Schulz Michael Shirts Alexey Shvetsov Alfons Sijbers Peter Tieleman Jon Vincent Teemu Virolainen Christian Wennberg Maarten Wolf Artem Zhmurov and the project leaders: Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel ``` Copyright (c) 1991-2000, University of Groningen, The Netherlands. Copyright (c) 2001-2019, The GROMACS development team at Uppsala University, Stockholm University and the Royal Institute of Technology, Sweden. check out [http://www.gromacs.org](http://www.gromacs.org) for more information. GROMACS is free software; you can redistribute it and/or modify it under the terms of the GNU Lesser General Public License as published by the Free Software Foundation; either version 2.1 of the License, or (at your option) any later version. GROMACS: gmx grompp, version 2021.4-Ubuntu-2021.4-2 Executable: /usr/bin/gmx Data prefix: /usr Working dir: /home/ruhul/Documents/glucosidase\_acarbose Command line: gmx grompp -f em.mdp -c complex\_solv\_ions.gro -p topol.top -o em.tpr Ignoring obsolete mdp entry ‘title’ Ignoring obsolete mdp entry ‘ns\_type’ NOTE 1 [file em.mdp]: With Verlet lists the optimal nstlist is \>= 10, with GPUs \>= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. Setting the LD random seed to 2108389175 Generated 167799 of the 167910 non-bonded parameter combinations Generating 1-4 interactions: fudge = 1 Generated 117432 of the 167910 1-4 parameter combinations Excluding 3 bonded neighbours molecule type ‘Protein\_chain\_A’ Excluding 3 bonded neighbours molecule type ‘UNK1’ Excluding 2 bonded neighbours molecule type ‘SOL’ Excluding 3 bonded neighbours molecule type ‘NA’ Analysing residue names: There are: 844 Protein residues There are: 1 Other residues There are: 34648 Water residues There are: 28 Ion residues Analysing Protein… Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups… Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups… Number of degrees of freedom in T-Coupling group rest is 247413.00 Calculating fourier grid dimensions for X Y Z Using a fourier grid of 100x100x100, spacing 0.119 0.119 0.119 Estimate for the relative computational load of the PME mesh part: 0.14 This run will generate roughly 9 Mb of data There was 1 note GROMACS reminds you: “Big Data is like teenage sex: everyone talks about it, nobody really knows how to do it, everyone thinks everyone else is doing it, so everyone claims they are doing it…” (Dan Ariely) ruhul@ruhul:~/Documents/glucosidase\_acarbose$ gmx mdrun -v -deffnm em :-) GROMACS - gmx mdrun, 2021.4-Ubuntu-2021.4-2 (-: ``` GROMACS is written by: Andrey Alekseenko Emile Apol Rossen Apostolov Paul Bauer Herman J.C. Berendsen Par Bjelkmar Christian Blau Viacheslav Bolnykh Kevin Boyd Aldert van Buuren Rudi van Drunen Anton Feenstra Gilles Gouaillardet Alan Gray Gerrit Groenhof Anca Hamuraru Vincent Hindriksen M. Eric Irrgang Aleksei Iupinov Christoph Junghans Joe Jordan Dimitrios Karkoulis Peter Kasson Jiri Kraus Carsten Kutzner Per Larsson Justin A. Lemkul Viveca Lindahl Magnus Lundborg Erik Marklund Pascal Merz Pieter Meulenhoff Teemu Murtola Szilard Pall Sander Pronk Roland Schulz Michael Shirts Alexey Shvetsov Alfons Sijbers Peter Tieleman Jon Vincent Teemu Virolainen Christian Wennberg Maarten Wolf Artem Zhmurov and the project leaders: Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel ``` Copyright (c) 1991-2000, University of Groningen, The Netherlands. Copyright (c) 2001-2019, The GROMACS development team at Uppsala University, Stockholm University and the Royal Institute of Technology, Sweden. check out [http://www.gromacs.org](http://www.gromacs.org) for more information. GROMACS is free software; you can redistribute it and/or modify it under the terms of the GNU Lesser General Public License as published by the Free Software Foundation; either version 2.1 of the License, or (at your option) any later version. GROMACS: gmx mdrun, version 2021.4-Ubuntu-2021.4-2 Executable: /usr/bin/gmx Data prefix: /usr Working dir: /home/ruhul/Documents/glucosidase\_acarbose Command line: gmx mdrun -v -deffnm em hwloc/linux: Ignoring PCI device with non-16bit domain. Pass --enable-32bits-pci-domain to configure to support such devices (warning: it would break the library ABI, don’t enable unless really needed). Compiled SIMD: SSE4.1, but for this host/run AVX\_512 might be better (see log). Reading file em.tpr, VERSION 2021.4-Ubuntu-2021.4-2 (single precision) Using 1 MPI thread Using 4 OpenMP threads Steepest Descents: Tolerance (Fmax) = 1.00000e+03 Number of steps = 50000 WARNING: Listed nonbonded interaction between particles 1708 and 1723 at distance 3.088 which is larger than the table limit 2.200 nm. This is likely either a 1,4 interaction, or a listed interaction inside a smaller molecule you are decoupling during a free energy calculation. Since interactions at distances beyond the table cannot be computed, they are skipped until they are inside the table limit again. You will only see this message once, even if it occurs for several interactions. IMPORTANT: This should not happen in a stable simulation, so there is probably something wrong with your system. Only change the table-extension distance in the mdp file if you are really sure that is the reason. WARNING: Listed nonbonded interaction between particles 10657 and 10668 at distance 2.240 which is larger than the table limit 2.200 nm. This is likely either a 1,4 interaction, or a listed interaction inside a smaller molecule you are decoupling during a free energy calculation. Since interactions at distances beyond the table cannot be computed, they are skipped until they are inside the table limit again. You will only see this message once, even if it occurs for several interactions. IMPORTANT: This should not happen in a stable simulation, so there is probably something wrong with your system. Only change the table-extension distance in the mdp file if you are really sure that is the reason. Step= 0, Dmax= 1.0e-02 nm, Epot= 1.12842e+06 Fmax= 8.55878e+05, atom= 1721 Step= 1, Dmax= 1.0e-02 nm, Epot= 1.05464e+06 Fmax= 8.45427e+05, atom= 1721 Step= 2, Dmax= 1.2e-02 nm, Epot= 9.82093e+05 Fmax= 8.33549e+05, atom= 1721 Step= 3, Dmax= 1.4e-02 nm, Epot= 9.08068e+05 Fmax= 8.20059e+05, atom= 1721 Step= 4, Dmax= 1.7e-02 nm, Epot= 8.30460e+05 Fmax= 8.04537e+05, atom= 1721 Step= 5, Dmax= 2.1e-02 nm, Epot= 7.47492e+05 Fmax= 7.86157e+05, atom= 1721 Step= 6, Dmax= 2.5e-02 nm, Epot= 6.57615e+05 Fmax= 7.63404e+05, atom= 1721 Step= 7, Dmax= 3.0e-02 nm, Epot= 5.59553e+05 Fmax= 7.33839e+05, atom= 1721 Step= 8, Dmax= 3.6e-02 nm, Epot= 4.52647e+05 Fmax= 6.94270e+05, atom= 1721 Step= 9, Dmax= 4.3e-02 nm, Epot= 3.38191e+05 Fmax= 6.41107e+05, atom= 1721 Step= 10, Dmax= 5.2e-02 nm, Epot= 2.21109e+05 Fmax= 5.74613e+05, atom= 1723 Step= 11, Dmax= 6.2e-02 nm, Epot= 1.27301e+05 Fmax= 4.13466e+06, atom= 1721 Step= 12, Dmax= 7.4e-02 nm, Epot= 1.05686e+05 Fmax= 5.12493e+05, atom= 1721 Step= 13, Dmax= 8.9e-02 nm, Epot= -4.82345e+04 Fmax= 1.12132e+06, atom= 1721 Step= 15, Dmax= 5.3e-02 nm, Epot= -8.49790e+04 Fmax= 7.07140e+05, atom= 1721 Step= 16, Dmax= 6.4e-02 nm, Epot= -1.35405e+05 Fmax= 5.68419e+05, atom= 1721 Step= 17, Dmax= 7.7e-02 nm, Epot= -2.06407e+05 Fmax= 5.05072e+05, atom= 1721 Step= 18, Dmax= 9.2e-02 nm, Epot= -2.85788e+05 Fmax= 4.82860e+05, atom= 1721 Step= 19, Dmax= 1.1e-01 nm, Epot= -3.75818e+05 Fmax= 1.25992e+06, atom= 10668 Step= 20, Dmax= 1.3e-01 nm, Epot= -3.89227e+05 Fmax= 3.14067e+05, atom= 10668 Step= 21, Dmax= 1.6e-01 nm, Epot= -4.49212e+05 Fmax= 8.62527e+06, atom= 1723 Step= 22, Dmax= 1.9e-01 nm, Epot= -5.00556e+05 Fmax= 3.38298e+06, atom= 1368 Step= 23, Dmax= 2.3e-01 nm, Epot= -5.38831e+05 Fmax= 2.53930e+05, atom= 1723 Step= 24, Dmax= 2.8e-01 nm, Epot= -7.45281e+05 Fmax= 9.59912e+05, atom= 10668 Segmentation fault (core dumped) Sir, May I know how to solve this?