[gmx-developers] multiple xtc output files (optionally in chunks)

Berk Hess hessb at mpip-mainz.mpg.de
Fri Oct 19 14:23:24 CEST 2007

Carsten Kutzner wrote:

>I wonder if we could have some new options for the XTC output of
>trajectories (I would also volunteer to implement them).
>The problem that we face in our group is the following. Since we do not
>use a queueing system, the trajectories naturally get very large. This
>is a headache for our backup system which has to backup each open file
>as a whole, even if only a few bytes were added since the last backup.
>What would be a nice solution is to allow two (or better multiple) XTC
>output files with individual options (nstxtcout1, xtc-grps1,
>nstxtcout2,..., similar to the new mdp pull options) and an extra
>parameter nstxtcchop1 for when to close an XTC and start writing to a
>new one.
>You could then e.g. save your protein *without* water in one single,
>small XTC file (nstxtcchop1=0) which is kept on disk for further
>analysis, while the large trajectory with water is saved in several
>chunks (and e.g. archived).
>Please let me know what you think.
>  Carsten
Multiple xtc files for different groups could in be useful, but I have never
had a need for this, nor did I get any requests.
I think chopping up files is useless.
The much easier solution here is to chop up your whole simulation in parts
and use tpbconv to continue runs, just like when you would have a queing 
(which you should install in Gottingen anyhow).


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