[gmx-users] any chance to write avoid writing out trr but only xtc file ?

Justin A. Lemkul jalemkul at vt.edu
Tue Dec 1 16:46:24 CET 2009

Jörn-Benjamin Lenz wrote:
> dear users of gromacs,
> i updated my gromacs from 4.0.1 to 4.0.5 and now i am facing the following problem:

Good move, version 4.0.1 was badly broken :)

> using the older version of gromacs I submitted REMD jobs to our cluster (which also was updated from suse 10.3 to suse 11.1) and two differently formatted output files were generated: trr files and xtc files
> since we always are short on disk space in our home folders i did the following:
> the trr files were written to the a folder in my home directory on our fileserver whereas the xtc files were written to the local machine i was using. in order to save disk storage on our fileserver (i.e. in /home/joern/...) i deleted the trr files once as soon as they were produced and the job on our cluster was still happy and wrote the xtc files to my local machine and i was very happy with that behaviour.
> using gromacs 4.0.5, again trr and xtc files are written. however, as soon as i delete the trr files the mdrun jobs die and the whole job finishes without keep on writing the xtc files as it did with the older version.
> is there  a chance to say gromacs not to write out a trr file at all but only a xtc file. without using the mdrun -o command gromacs still writes out the standard trajX.trr files. or is this becuase of the update from suse 10.3 to suse 11.1 ?

I don't think you can completely suppress the output, but you can certainly 
reduce the size of the output files using very large values of nstxout, and 
nstvout, for example.


> any help and / or advice is much appreciated !
> many thanks in advance,
> joern


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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