# What causes can disrupt the msd calculation process?

**URL:** <https://gromacs.bioexcel.eu/t/what-causes-can-disrupt-the-msd-calculation-process/1709>\
**Category:** User discussions\
**Tags:** analysis-tools\
**Created:** [March 8, 2021, 8:09am UTC](https://gromacs.bioexcel.eu/t/what-causes-can-disrupt-the-msd-calculation-process/1709 "2021-03-08T08:09:19Z")\
**Posts on this page:** 4\
**Page:** 1

<div class="post-metadata">

**Author:** ![biotech70](https://avatars.discourse-cdn.com/v4/letter/b/a4c791/32.png) [@biotech70](https://gromacs.bioexcel.eu/u/biotech70)\
**Post date:** [March 8, 2021, 8:09am UTC](https://gromacs.bioexcel.eu/t/what-causes-can-disrupt-the-msd-calculation-process/1709/1 "2021-03-08T08:09:19Z")

</div>

GROMACS version:2021  
GROMACS modification: Yes/No  
Here post your question  
I have done 200 ns MD for membranes and nanoparticles and I want to do the MSD calculations, but in the 194 ns process was killed. What is the cause and how is it solved?

---

<div class="post-metadata">

**Author:** ![milosz.wieczor](https://avatars.discourse-cdn.com/v4/letter/m/b19c9b/32.png) [@milosz.wieczor](https://gromacs.bioexcel.eu/u/milosz.wieczor)\
**Post date:** [March 8, 2021, 3:58pm UTC](https://gromacs.bioexcel.eu/t/what-causes-can-disrupt-the-msd-calculation-process/1709/2 "2021-03-08T15:58:51Z")

</div>

Hard to say with limited data, but on login nodes of many clusters, admins will often automatically kill analysis jobs that run for longer than some threshold. I imagine this might be your case.

Anyway, how is the title related to the actual question?

---

<div class="post-metadata">

**Author:** ![biotech70](https://avatars.discourse-cdn.com/v4/letter/b/a4c791/32.png) [@biotech70](https://gromacs.bioexcel.eu/u/biotech70)\
**Post date:** [March 8, 2021, 6:06pm UTC](https://gromacs.bioexcel.eu/t/what-causes-can-disrupt-the-msd-calculation-process/1709/3 "2021-03-08T18:06:01Z")

</div>

thanks for your response. I do the calculations on my personal system and I am the admin.

---

<div class="post-metadata">

**Author:** ![kevinboyd](https://avatars.discourse-cdn.com/v4/letter/k/c77e96/32.png) [@kevinboyd](https://gromacs.bioexcel.eu/u/kevinboyd)\
**Post date:** [March 17, 2021, 3:11pm UTC](https://gromacs.bioexcel.eu/t/what-causes-can-disrupt-the-msd-calculation-process/1709/4 "2021-03-17T15:11:29Z")

</div>

Hi, this is almost certainly an out-of-memory error. gmx msd has to save every frame to back-calculate long MSDs, and you’re probably hitting a limit.

Right now, you can reduce the number of frames saved by increasing the value of the -trestart option.

In Gromacs 2022, I’m planning to add an option to cap the max “tau” value for MSD comparison, to reduce memory, but that won’t be available for a while.