[gmx-users] Huge trr files

[David Mobley]

It all depends on what you want to do with the output. In order to be
able to restart runs, you need to have some restart files with
velocities (i.e. in case of crash), which means you need *some* frames
in your trr files. Also, xtc files aren't full precision, so if you
want anything that requires full precision (i.e. being able to
reprocess trajectories, or compute some parameter which is extremely
sensitive to distances) then you need to use trr files. On the other
hand, if all you care about is being able to see roughly what happens
in your system, you're free to use only xtc files. A usual compromise
for me is to write more frames to xtc files and fewer to trr files.

Also, 0.5 ps sounds fairly short to me. A general rule of thumb for me
is that you don't need to bother writing frames that are a lot shorter
than the correlation time for your system, since frames will be
strongly correlated. If you have an idea how long the correlation time
is, you can adjust your output frequency accordingly.

A final trick to reduce the size is to only write some component of
the system to output (I think there is an output groups option in the
input file).

Lastly, decide how much space you can afford to spend on your output
files, and adjust your output parameters accordingly.

David



On 1/30/06, hseara at netscape.net <hseara at netscape.net> wrote:
>
> Dear gmx users,
>
> I've been performing different dynamics on lipid monolayers. My problem is
> that the output files *.trr are huge, up to 80 GB. Do you think it is enough
> to maintain the xtc files for the analysis or there are properties which are
> unable to be calculated with the precision given by the xtc file?. If I
> really need the trr file, any one know how to cut it in several files to be
> able to work with them properly.
> Also I've been saving every 0,5 ps. Maybe is so short this saving time?
> someone knows which is the usual saving time in monolayer/ bilayer systems?
>
> Thanks a lot
>
> Hector
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