# QM/MM simulation crashes with segmentation fault when running it a second time

**URL:** <https://ask.bioexcel.eu/t/qm-mm-simulation-crashes-with-segmentation-fault-when-running-it-a-second-time/4254>\
**Category:** QM/MM for Biomolecular Simulation\
**Created:** [April 11, 2023, 8:23am UTC](https://ask.bioexcel.eu/t/qm-mm-simulation-crashes-with-segmentation-fault-when-running-it-a-second-time/4254 "2023-04-11T08:23:38Z")\
**Posts on this page:** 3\
**Page:** 1

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**Author:** ![hpoggemann](https://avatars.discourse-cdn.com/v4/letter/h/49beb7/32.png) [@hpoggemann](https://ask.bioexcel.eu/u/hpoggemann)\
**Post date:** [April 11, 2023, 8:23am UTC](https://ask.bioexcel.eu/t/qm-mm-simulation-crashes-with-segmentation-fault-when-running-it-a-second-time/4254/1 "2023-04-11T08:23:38Z")

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Dear all,

I am trying to run QM/MM simulations of an enzyme with an cysteine bound ferric heme in the centre and I came across a strange problem with my simulations: I did run an energy minimisation once that completed, but when I restart it a second time the simulation crashes with segmentation fault error.  
Since I am quite new to QM/MM simulations I am not sure if there is a problem with my input or if the gromacs + CP2K interface on the cluster has a bug.

I did create a folder in my owncloud with all the input files I am using, so you can have a look at my parameters. I would be very glad about any tip on my issue.

> **[ownCloud - A safe home for all your data](https://www.theoechem.org/owncloud/index.php/s/gZR6A1u5tgjaDty)**
>
> QMMM is publicly shared

Best,  
Hanna

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**Author:** ![dmorozov](https://avatars.discourse-cdn.com/v4/letter/d/dec6dc/32.png) [@dmorozov](https://ask.bioexcel.eu/u/dmorozov)\
**Post date:** [April 19, 2023, 3:25pm UTC](https://ask.bioexcel.eu/t/qm-mm-simulation-crashes-with-segmentation-fault-when-running-it-a-second-time/4254/2 "2023-04-19T15:25:54Z")

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Hi, Try to put more atoms into QM part. For Cysteine at least S-CH2 should be included

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**Author:** ![hpoggemann](https://avatars.discourse-cdn.com/v4/letter/h/49beb7/32.png) [@hpoggemann](https://ask.bioexcel.eu/u/hpoggemann)\
**Post date:** [May 3, 2023, 7:58am UTC](https://ask.bioexcel.eu/t/qm-mm-simulation-crashes-with-segmentation-fault-when-running-it-a-second-time/4254/3 "2023-05-03T07:58:29Z")

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I included the atoms you suggested and now it kinda works. At least when I am using the BLYP functional. Strangely I still get segmentation faults when I am using PBE. I did just try it as a test but do you have any guess why this is happening?