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

chris.neale at utoronto.ca chris.neale at utoronto.ca
Wed Dec 2 15:17:00 CET 2009

We have the same desire on a large cluster in order to reduce the  
number of file operations overall. In addition to Xavier's suggestion,  
you can also write your .trr to memory:
mdrun -deffnm xx -t /dev/shm/xx.trr
or to the local disk:
mdrun -deffnm xx -t ${TMPDIR}/xx.trr
if those exist and depending on your architecture. Contact your  
sysadmin for the best option here... just be sure to rm -f your  
unwanted .trr.

While I agree that the ability to not create the .trr at all or to  
write the .trr to /dev/null would be ideal, that appears to be  
incompatible with the automated file name extension determination and  
the provided solution will probably be just as fast.


-- original message --

you can define the frequency of writing to the trr file in the mdp file.


nstxout = 0
nstvout = 0
nstfout =0

should fix your problem.

On Dec 1, 2009, at 4:30 PM, 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:
> 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,
> joern
> --

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