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

David van der Spoel spoel at xray.bmc.uu.se
Fri Oct 19 14:48:24 CEST 2007

Berk Hess wrote:
> Carsten Kutzner wrote:
>> Hi,
>> 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.
>> Regards,
>>  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 
> system
> (which you should install in Gottingen anyhow).
I agree, but what we should implement, and what is also on the todo list 
on the wiki, is to be able to analyze N trajectories as one, e.g. 
g_hbond -f a.xtc b.xtc c.xtc and so on.

David van der Spoel, Ph.D.
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205. Fax: +4618511755.
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se

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