# Continuing simulation after timeout

**URL:** <https://gromacs.bioexcel.eu/t/continuing-simulation-after-timeout/8122>\
**Category:** User discussions\
**Tags:** mdrun, simulation-setup\
**Created:** [January 24, 2024, 2:35am UTC](https://gromacs.bioexcel.eu/t/continuing-simulation-after-timeout/8122 "2024-01-24T02:35:27Z")\
**Posts on this page:** 2\
**Page:** 1

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**Author:** ![cjbraz](https://avatars.discourse-cdn.com/v4/letter/c/b9bd4f/32.png) [@cjbraz](https://gromacs.bioexcel.eu/u/cjbraz)\
**Post date:** [January 24, 2024, 2:35am UTC](https://gromacs.bioexcel.eu/t/continuing-simulation-after-timeout/8122/1 "2024-01-24T02:35:27Z")

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GROMACS version: 2020.3  
GROMACS modification: No  
Here post your question

I am attempting to continue a simulation from when it timed out. My simulation made it to production and has a step5\_1\_prev.cpt file. I am using a script from CHARMM-GUI and am having issues with modifying it. I thought about commenting out the minimization and equilibration steps first. Should I add the -cpi flag to each of the lines in my production script?

Please see the copied link for github repository. I tried pasting the code in this forum and the result was not pretty. Thank you!

> <https://github.com/cjbrazdaz/gromacs2020.3_cont/commit/51e991b06b9c0f234dd620cabbc45aa7760f249c>

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**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:** [January 24, 2024, 8:16am UTC](https://gromacs.bioexcel.eu/t/continuing-simulation-after-timeout/8122/2 "2024-01-24T08:16:35Z")

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Yes, you should add the `-cpi <filename>` option to avoid overwriting what is already finished.

I would suggest commenting out the lines starting the steps that are finished, but as long as you provide checkpoint files it does not make much difference. You will get a new copy of the final configuration and lose the performance information in the log file if you run the finished jobs.