# Segmentation fault on mdrun

**URL:** <https://gromacs.bioexcel.eu/t/segmentation-fault-on-mdrun/7090>\
**Category:** User discussions\
**Created:** [August 28, 2023, 8:42am UTC](https://gromacs.bioexcel.eu/t/segmentation-fault-on-mdrun/7090 "2023-08-28T08:42:14Z")\
**Posts on this page:** 2\
**Page:** 1

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**Author:** ![HyewonLee](https://avatars.discourse-cdn.com/v4/letter/h/6a8cbe/32.png) [@HyewonLee](https://gromacs.bioexcel.eu/u/HyewonLee)\
**Post date:** [August 28, 2023, 8:42am UTC](https://gromacs.bioexcel.eu/t/segmentation-fault-on-mdrun/7090/1 "2023-08-28T08:42:14Z")

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GROMACS version: 2023.2  
GROMACS modification: Yes/No

Hi,

1. I’m wondering if ‘LINCS WARNING’ is showing up as ‘segmentation fault’ in version 2023.2. My guess is that in version 22.4, I could see a similar error with LINCS WARNING message, but since using version 23.2, I haven’t seen the phrase LINCS WARNING in the err log.

2. I’m simulating a polyphenol molecule. The .itp file was newly generated by ATB ([https://atb.uq.edu.au/index.py](https://atb.uq.edu.au/index.py)).

I added water and ions to the ligand without proteins. I used gromos54a7 and spc. I can’t change ff because the topology builder (ATB) site limits ff to gromos54a7.

I keep getting the error message below in the MD step after the EM, NPT, NVT steps. The simulation fails to complete and aborts.

* * *

## starting mdrun ‘ALL0 in water’ 5530000 steps, 11060.0 ps (continuing from step 530000, 1060.0 ps). train.sh: line 21: 1475476 Segmentation fault (core dumped) gmx mdrun -deffnm md1

I attach the em, npt, nvt, md.mdp files I used.

Thanks.

[em.mdp](https://gromacs.bioexcel.eu/uploads/short-url/w256Gl4wbvrEbBb4uoI0I25FkPA.mdp) (1.2 KB)  
[md.mdp](https://gromacs.bioexcel.eu/uploads/short-url/7xRTO2fmII7rpuV1tBKmKJ5TSSc.mdp) (2.2 KB)  
[npt.mdp](https://gromacs.bioexcel.eu/uploads/short-url/xmYamxNhQKcNdzxQl16wn7F5c3o.mdp) (2.2 KB)  
[nvt.mdp](https://gromacs.bioexcel.eu/uploads/short-url/dNLkQXwJiZLsumkWeRd3ZquLZ7v.mdp) (2.2 KB)

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<div class="post-metadata">

**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:** [August 29, 2023, 6:24am UTC](https://gromacs.bioexcel.eu/t/segmentation-fault-on-mdrun/7090/2 "2023-08-29T06:24:43Z")

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This is almost certainly the system that is exploding. I would suggest the following to see if it helps:

In md.mdp:  
The reason why I think your system crashes is because of oscillations caused by your low `tau-p` with a Parrinello-Rahman barostat. Switch to `c-rescale` instead. `c-rescale` can be used for both equilibration and production.  
See also my suggestions for npt.mdp below.

I addition I would recommend the following changes, especially if the above did not help.

In em.mdp:  
Turn on the position restraints for protein and ligand (`define = -DPOSRES -DPOSRES_LIG`)  
Increase `nsteps` to 25,000 and check the log output.

In nvt.mdp:  
Also here I would suggest using position restraint for protein and ligand.  
Increase nsteps to 100,000.  
Set `constraints = hbond`.  
I would also argue that you don’t need annealing to heat the system.  
I think your `tau-t` is unnecessarily low. I think you would do fine with 1ps.

In npt.mdp:  
Here I also suggest a higher `tau-t` and to only constrain the hydrogen bonds.

I hope that helps.