# System crash on running energy minimzation on dimer solvated in water

**URL:** <https://gromacs.bioexcel.eu/t/system-crash-on-running-energy-minimzation-on-dimer-solvated-in-water/8026>\
**Category:** User discussions\
**Tags:** mdrun\
**Created:** [January 12, 2024, 7:39am UTC](https://gromacs.bioexcel.eu/t/system-crash-on-running-energy-minimzation-on-dimer-solvated-in-water/8026 "2024-01-12T07:39:54Z")\
**Posts on this page:** 3\
**Page:** 1

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**Author:** ![meenakshitellis](https://avatars.discourse-cdn.com/v4/letter/m/13edae/32.png) [@meenakshitellis](https://gromacs.bioexcel.eu/u/meenakshitellis)\
**Post date:** [January 12, 2024, 7:39am UTC](https://gromacs.bioexcel.eu/t/system-crash-on-running-energy-minimzation-on-dimer-solvated-in-water/8026/1 "2024-01-12T07:39:54Z")

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Hello,  
I want to perform REMD simulations on a protein dimer solvated in different concentrations of urea. For this, first to create only water system I have created box and solvated in water. When I was running energy minimization, the system got crashed and got below error. The two monomers are placed at a distance in the system.  
GROMACS: gmx mdrun, version 2021.4-Ubuntu-2021.4-2  
Executable: /usr/bin/gmx  
Data prefix: /usr  
Working dir: /home/ubuntu/Meenakshi/REMD-simulations/bcn-water  
Command line:  
gmx mdrun -v -deffnm em

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 16 OpenMP threads

Steepest Descents:  
Tolerance (Fmax) = 1.00000e+03  
Number of steps = 50000

WARNING: Listed nonbonded interaction between particles 3910 and 3918  
at distance 2.751 which is larger than the table limit 2.000 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= 1.27151e+33 Fmax= inf, atom= 4719  
Segmentation fault (core dumped)

What can this be due to? How can I resolve it?

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<div class="post-metadata">

**Author:** ![meenakshitellis](https://avatars.discourse-cdn.com/v4/letter/m/13edae/32.png) [@meenakshitellis](https://gromacs.bioexcel.eu/u/meenakshitellis)\
**Post date:** [January 12, 2024, 12:17pm UTC](https://gromacs.bioexcel.eu/t/system-crash-on-running-energy-minimzation-on-dimer-solvated-in-water/8026/2 "2024-01-12T12:17:49Z")

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I have placed the two monomers such that they are 5 angstroms apart.

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**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:** [January 12, 2024, 1:46pm UTC](https://gromacs.bioexcel.eu/t/system-crash-on-running-energy-minimzation-on-dimer-solvated-in-water/8026/3 "2024-01-12T13:46:02Z")

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Please post in the User discussions section of the forum, not site feedback. You will need to provide more details, such as what the system is, how you prepared it, if `pdb2gmx` had any issues, etc.