[gmx-users] RAM usage of gmx msd

Martin Kern martin.kern at uni-konstanz.de
Tue Sep 17 08:53:28 CEST 2019

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 

I found an old email that also mentions the high RAM usage of gmx msd 
but it didn't get a reply.

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

I'm grateful for any suggestion.

Best regards
Martin Kern

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