# Energy minimization is not completing properly

**URL:** https://gromacs.bioexcel.eu/t/energy-minimization-is-not-completing-properly/4492
**Category:** User discussions
**Tags:** mdrun
**Created:** [July 22, 2022, 10:37am UTC](https://gromacs.bioexcel.eu/t/energy-minimization-is-not-completing-properly/4492 "2022-07-22T10:37:57Z")
**Posts on this page:** 1
**Page:** 1

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### Author: ![Kankana](https://avatars.discourse-cdn.com/v4/letter/k/7993a0/32.png) [@Kankana](https://gromacs.bioexcel.eu/u/Kankana)
#### Post date: [July 22, 2022, 10:37am UTC](https://gromacs.bioexcel.eu/t/energy-minimization-is-not-completing-properly/4492/1 "2022-07-22T10:37:57Z")

</div>

GROMACS version: 2020.1  
GROMACS modification: No

Dear GROMACS Developers,

I, Ms Kankana Bhattacharjee, pursuing Ph. D. from Ashoka University, performing energy minimization of water-propanol system. At first, initial configurations were created using Packmol. Commands used for energy minimization step as follows:  
gmx grompp -f em.mdp -c water-propanol-box.gro -p topol.top -o em.tpr  
em.mdp:  
; minim.mdp - used as input into grompp to generate em.tpr  
; Parameters describing what to do, when to stop and what to save  
integrator = steep ; Algorithm (steep = steepest descent minimization)  
emtol = 1000.0 ; Stop minimization when the maximum force \< 1000.0 kJ/mol/nm  
emstep = 0.01 ; Minimization step size  
nsteps = 50000 ; Maximum number of (minimization) steps to perform

; Parameters describing how to find the neighbors of each atom and how to calculate the interactions  
nstlist = 1 ; Frequency to update the neighbor list and long range forces  
cutoff-scheme = Verlet ; Buffered neighbor searching  
ns\_type = grid ; Method to determine neighbor list (simple, grid)  
coulombtype = PME ; Treatment of long range electrostatic interactions  
rcoulomb = 1.0 ; Short-range electrostatic cut-off  
rvdw = 1.0 ; Short-range Van der Waals cut-off  
pbc = xyz ; Periodic Boundary Conditions in all 3 dimensions  
after that,  
gmx mdrun -v -deffnm em

Steepest Descents:  
Tolerance (Fmax) = 1.00000e+03  
Number of steps = 50000  
Step= 0, Dmax= 1.0e-02 nm, Epot= 1.65985e+08 Fmax= 3.61065e+08, atom= 920  
Step= 1, Dmax= 1.0e-02 nm, Epot= 1.39384e+08 Fmax= 7.97155e+07, atom= 605  
Step= 2, Dmax= 1.2e-02 nm, Epot= 8.56262e+07 Fmax= 2.17396e+07, atom= 605  
Step= 3, Dmax= 1.4e-02 nm, Epot= 4.39698e+07 Fmax= 6.79498e+06, atom= 18579  
Step= 4, Dmax= 1.7e-02 nm, Epot= 2.22925e+07 Fmax= 2.54006e+06, atom= 6147  
Step= 5, Dmax= 2.1e-02 nm, Epot= 1.19056e+07 Fmax= 2.08284e+06, atom= 11379  
Step= 6, Dmax= 2.5e-02 nm, Epot= 8.52987e+06 Fmax= 1.90028e+06, atom= 5367  
Step= 7, Dmax= 3.0e-02 nm, Epot= 6.60448e+06 Fmax= 6.53105e+05, atom= 12900  
Step= 8, Dmax= 3.6e-02 nm, Epot= 3.81999e+06 Fmax= 1.41957e+06, atom= 5367  
Step= 9, Dmax= 4.3e-02 nm, Epot= 3.32901e+06 Fmax= 1.37722e+05, atom= 6231  
Step= 10, Dmax= 5.2e-02 nm, Epot= 1.13227e+06 Fmax= 2.05470e+05, atom= 19770  
Step= 11, Dmax= 6.2e-02 nm, Epot= 8.70744e+05 Fmax= 6.56116e+05, atom= 3246  
Step= 12, Dmax= 7.4e-02 nm, Epot= 8.01573e+05 Fmax= 1.17045e+06, atom= 2529  
Step= 13, Dmax= 8.9e-02 nm, Epot= 7.44644e+05 Fmax= 3.90100e+04, atom= 19770  
Segmentation fault  
I am unable to figure out, why “Segmentation fault” is coming.

Regards  
Kankana Bhattacharjee  
Ph. D. Scholar  
Department of Chemistry  
Ashoka University  
Sonipat, Haryana