# Segementation error while running em **URL:** \ **Category:** User discussions\ **Tags:** mdrun\ **Created:** [June 23, 2021, 4:54am UTC](https://gromacs.bioexcel.eu/t/segementation-error-while-running-em/2400 "2021-06-23T04:54:30Z")\ **Posts on this page:** 4\ **Page:** 1
**Author:** ![rijja](https://avatars.discourse-cdn.com/v4/letter/r/4491bb/32.png) [@rijja](https://gromacs.bioexcel.eu/u/rijja)\ **Post date:** [June 23, 2021, 4:54am UTC](https://gromacs.bioexcel.eu/t/segementation-error-while-running-em/2400/1 "2021-06-23T04:54:30Z")
GROMACS version:2019 GROMACS modification: No Here post your question : I run the cammand “gmx mdrun -v -deffnm em” and getting this output: ``` :-) GROMACS - gmx mdrun, 2019.6 (-: GROMACS is written by: 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 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 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) 2001-2018, 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 2019.6 Executable: /share/apps/packages/gromacs/installation/bin/gmx Data prefix: /share/apps/packages/gromacs/installation Working dir: /export/ Command line: gmx mdrun -deffnm em -v Back Off! I just backed up em.log to ./#em.log.2# Reading file em.tpr, VERSION 2019.6 (single precision) Using 1 MPI process Using 24 OpenMP threads 1 GPU selected for this run. Mapping of GPU IDs to the 1 GPU task in the 1 rank on this node: PP:0 PP tasks will do (non-perturbed) short-ranged interactions on the GPU Back Off! I just backed up em.trr to ./#em.trr.2# Back Off! I just backed up em.edr to ./#em.edr.2# Steepest Descents: Tolerance (Fmax) = 1.00000e+05 Number of steps = 50000 Step= 0, Dmax= 1.0e-02 nm, Epot= 1.55967e+35 Fmax= inf, atom= 42 Segmentation fault i have check my server my job run for few seconds and then end. Kindly guide. ---
**Author:** ![fkeller](https://avatars.discourse-cdn.com/v4/letter/f/ba9def/32.png) [@fkeller](https://gromacs.bioexcel.eu/u/fkeller)\ **Post date:** [June 23, 2021, 9:51am UTC](https://gromacs.bioexcel.eu/t/segementation-error-while-running-em/2400/2 "2021-06-23T09:51:21Z")
Dear Rija, this is due to high forces appearing in your em (see line “Step= 0, Dmax= 1.0e-02 nm, Epot= 1.55967e+35 Fmax= inf, atom= 42” → Fmax=inf) Something seems to be bad about your initial configuration and atom 42 seems to overlap with another one. Sometimes it helps not to use GPUs and few CPU cores, as (for me) using MPI and/or GPU seems to be more unstable. Best Fabian ---
**Author:** ![rijja](https://avatars.discourse-cdn.com/v4/letter/r/4491bb/32.png) [@rijja](https://gromacs.bioexcel.eu/u/rijja)\ **Post date:** [June 24, 2021, 5:25am UTC](https://gromacs.bioexcel.eu/t/segementation-error-while-running-em/2400/3 "2021-06-24T05:25:43Z")
Dear Fabian, Thanks for your help. Is there a way that I can change the coordinates of my overlapping atoms. Which file should I looked into or run again? As I am using gromacs on official system so CPU core option is not possible. Grateful, Rijja ---
**Author:** ![fkeller](https://avatars.discourse-cdn.com/v4/letter/f/ba9def/32.png) [@fkeller](https://gromacs.bioexcel.eu/u/fkeller)\ **Post date:** [June 24, 2021, 3:59pm UTC](https://gromacs.bioexcel.eu/t/segementation-error-while-running-em/2400/4 "2021-06-24T15:59:29Z")
Dear Rijja, yes, you can modify your input structure file (.pdb, .gro, …), though this is a tedious task. I recommend checking the protocol for creating your input structure file. Before you start important simulations I also highly recommend going through all or at least some of the [GROMACS Tutorials](http://www.mdtutorials.com/gmx/) to get used to the different file types and its contents of gromacs. Best Fabian