[gmx-users] Re: any chance to write avoid writing out trr but only xtc file ?
joern.lenz at screeningport.com
Tue Dec 1 19:39:03 CET 2009
thanks you xavier and justin for your answers on my problem,
however, i still wonder why i could completely delete the e.g. five trr files (from an REMD simulation on our cluster) named trajX.trr (with X = 0..4) and the corresponding xtc files (trajX.xtc) were still written out in one of the former gromacs versions.
now this is not possible any more, i.e. as soon as i delete one of the trajX.trr files, the whole simulation breaks.
does anyone know a reason for this behaviour and/or how i can fix this ?
many thanks and greetings,
>you can define the frequency of writing to the trr file in the mdp file.
>nstxout = 0
>nstvout = 0
>should fix your problem.
Am 01.12.2009 um 16:30 schrieb Jörn-Benjamin Lenz:
> dear users of gromacs,
> i updated my gromacs from 4.0.1 to 4.0.5 and now i am facing the following problem:
> 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 ?
> any help and / or advice is much appreciated !
> many thanks in advance,
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