# Restarted the simulation with checkpoint, but started from begining

**URL:** <https://gromacs.bioexcel.eu/t/restarted-the-simulation-with-checkpoint-but-started-from-begining/2185>\
**Category:** User discussions\
**Tags:** mdrun\
**Created:** [May 18, 2021, 11:33am UTC](https://gromacs.bioexcel.eu/t/restarted-the-simulation-with-checkpoint-but-started-from-begining/2185 "2021-05-18T11:33:07Z")\
**Posts on this page:** 4\
**Page:** 1

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**Author:** ![scinikhil](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/scinikhil/32/3483_2.png) [@scinikhil](https://gromacs.bioexcel.eu/u/scinikhil)\
**Post date:** [May 18, 2021, 11:33am UTC](https://gromacs.bioexcel.eu/t/restarted-the-simulation-with-checkpoint-but-started-from-begining/2185/1 "2021-05-18T11:33:08Z")

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GROMACS version:2021.2  
GROMACS modification: Yes  
Here post your question  
I am running a simulation on a supercomputer using 500 core. The simulation is stopped after the wall time. when I submitted the job with the correct checkpoint file, the simulation started from the beginning. It restarted the simulation and replaced all the previously written file. I don’t find anything unusual with the log file. Unfortunately, the GROMACS is modified and I do not have any information regarding that.  
(the commands are fine because later it worked fine )  
The simulation I have started from the different directory and it worked fine. However, the same error occurred for a couple of jobs.  
Any input would be helpful.

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**Author:** ![MichelePellegrino](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/michelepellegrino/32/628_2.png) [@MichelePellegrino](https://gromacs.bioexcel.eu/u/MichelePellegrino)\
**Post date:** [May 20, 2021, 6:46am UTC](https://gromacs.bioexcel.eu/t/restarted-the-simulation-with-checkpoint-but-started-from-begining/2185/2 "2021-05-20T06:46:51Z")

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Hi,

it’s difficult to tell what may be going wrong, especially since you are using a modified GROMACS version. Are you _explicitly_ adding the `-cpi` option when running `mdrun` and providign the correct checkpoint file name? In case the checkpoint file cannot be found `mdrun` would start the simulation from the beginning, and as far as I know `-cpi` is not a default option.

Michele

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**Author:** ![Bratin](https://avatars.discourse-cdn.com/v4/letter/b/f07891/32.png) [@Bratin](https://gromacs.bioexcel.eu/u/Bratin)\
**Post date:** [May 23, 2021, 4:56pm UTC](https://gromacs.bioexcel.eu/t/restarted-the-simulation-with-checkpoint-but-started-from-begining/2185/3 "2021-05-23T16:56:35Z")

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You need to give -append flag

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**Author:** ![scinikhil](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/scinikhil/32/3483_2.png) [@scinikhil](https://gromacs.bioexcel.eu/u/scinikhil)\
**Post date:** [May 23, 2021, 5:09pm UTC](https://gromacs.bioexcel.eu/t/restarted-the-simulation-with-checkpoint-but-started-from-begining/2185/4 "2021-05-23T17:09:44Z")

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No, usually, it should work with -cpi.  
The particular error occurred only during a certain period. It worked after that, so we suspect it is due to some other random reasons. We couldn’t reproduce the error even with same TPR file.