[gmx-users] RAM usage of gmx msd

Martin Kern martin.kern at uni-konstanz.de
Tue Sep 17 14:58:25 CEST 2019

Hi John,

thanks for your answer. The mdrun_key_atoms.xtc FILE is only around 500 
MB in size. But the issue here wasn't RAM usage but a segmentation 
fault. gmx msd requires a tpr file and I guess that my tpr and xtc files 
didn't fit together. Skipping frames might work without the need of a 
modified tpr file. I'll try that tomorrow.

Am 17.09.2019 um 12:09 schrieb John Whittaker:
> 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,
> John
>> I'm grateful for any suggestion.
>> Best regards
>> Martin Kern
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