# Error computing diffusion coefficient

**URL:** <https://gromacs.bioexcel.eu/t/error-computing-diffusion-coefficient/1052>\
**Category:** User discussions\
**Created:** [November 6, 2020, 10:51am UTC](https://gromacs.bioexcel.eu/t/error-computing-diffusion-coefficient/1052 "2020-11-06T10:51:36Z")\
**Posts on this page:** 3\
**Page:** 1

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**Author:** ![Teslim](https://avatars.discourse-cdn.com/v4/letter/t/f1d935/32.png) [@Teslim](https://gromacs.bioexcel.eu/u/Teslim)\
**Post date:** [November 6, 2020, 10:51am UTC](https://gromacs.bioexcel.eu/t/error-computing-diffusion-coefficient/1052/1 "2020-11-06T10:51:36Z")

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GROMACS version: 2018.1  
GROMACS modification: No  
I am trying to compute the diffusion coefficient using the gmx msd command.

> echo 1 | gmx msd -f mol\_A.nojump.mol.xtc -s em.tpr -o mol\_A\_msd.xvg

After initiating the command, I got the following  
Run 1

> Reading frame 56000 time 560200.000 Killed

Run 2

> Reading frame 88000 time 880200.000 srun: error: hpc005: task 0: Killed

What could be wrong? I check the trajectory using the gmx check command and the trajectory has the complete timesteps

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**Author:** ![kevinboyd](https://avatars.discourse-cdn.com/v4/letter/k/c77e96/32.png) [@kevinboyd](https://gromacs.bioexcel.eu/u/kevinboyd)\
**Post date:** [November 6, 2020, 9:06pm UTC](https://gromacs.bioexcel.eu/t/error-computing-diffusion-coefficient/1052/2 "2020-11-06T21:06:25Z")

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Hi - you likely ran out of memory, MSD calculations take a **lot** of memory. Try skipping some frames with the -trestart option.

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<div class="post-metadata">

**Author:** ![Teslim](https://avatars.discourse-cdn.com/v4/letter/t/f1d935/32.png) [@Teslim](https://gromacs.bioexcel.eu/u/Teslim)\
**Post date:** [November 7, 2020, 1:11pm UTC](https://gromacs.bioexcel.eu/t/error-computing-diffusion-coefficient/1052/3 "2020-11-07T13:11:57Z")

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Thanks for your suggestion. It worked!