[gmx-users] RAM usage of gmx msd

John Whittaker johnwhittake at zedat.fu-berlin.de
Tue Sep 17 12:09:49 CEST 2019

Hi Martin,

> Hello everyone.
> I simulated a cell membrane and would like to calculate lateral
> diffusion of lipids. I tried this using the gmx msd command.
> Unfortunately this uses enormous amounts of RAM. The process runs
> without error until it is killed by the operating system. No output file
> is created at that time.
> The membrane contains around 400 lipids and I simulated for 1100ns which
> is 220000 frames. The total size of the xtc file is around 150 GB. I use
> GROMACS 2016.4 with GPU support. The command I used was:
> gmx msd -s mdrun.tpr -f mdrun.xtc -n key_atoms.ndx -lateral z -o
> lateraal_diffusion.xvg
> I found an old email that also mentions the high RAM usage of gmx msd
> but it didn't get a reply.
> https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2018-January/118014.html
> I also tried reducing the RAM usage by creating a trajectory that only
> includes the key atoms. This attempt resulted in a segmentation fault.
> Here is what I tried:
> gmx trjconv -f mdrun.xtc -n key_atoms.ndx -o mdrun_key_atoms.xtc
> gmx convert-tpr -f mdrun.tpr -n key_atoms.ndx -o mdrun_key_atoms.tpr
> gmx msd -s mdrun_key_atoms.tpr -f mdrun_key_atoms.xtc -n key_atoms.ndx
> -lateral z -o lateraal_diffusion.xvg

How big is the "mdrun_key_atoms.xtc" trajectory? It's possible that this
file is still too large for the amount of RAM available on your machine.

Are you able to break this trajectory down into smaller chunks that are
more manageable? You could also use the -skip or -dt options of gmx
trjconv in order to write only every "n" frames.

Hope this helps,


> I'm grateful for any suggestion.
> Best regards
> Martin Kern
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