[gmx-users] RAM usage of gmx msd

[Mark Abraham]

Hi,

It's likely that using the same index file is the problem. The numbers it
contains are interpreted relative to the tpr file, so if you make a subset
of the tpr file, then it's on you to understand whether the necessary
indices have changed or not.

Mark

On Tue, 17 Sep 2019 at 14:58, Martin Kern <martin.kern at uni-konstanz.de>
wrote:

> 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
> >>
> >> --
> >> Gromacs Users mailing list
> >>
> >> * Please search the archive at
> >> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> >> posting!
> >>
> >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >>
> >> * For (un)subscribe requests visit
> >> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send
> >> a mail to gmx-users-request at gromacs.org.
> >>
> >
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
>