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

Justin A. Lemkul jalemkul at vt.edu
Tue Dec 1 19:59:17 CET 2009

Jörn-Benjamin Lenz wrote:
> 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

Do you get any sort of error?  I would think mdrun would at least report the I/O 
problem.  I don't know what the difference would be in this regard between the 
older and newer versions, but perhaps some changes were made such that mdrun 
expects all files standard output files to be present (perhaps to allow for the 
use of checkpointing?).  Just a guess, but certainly Xavier's solution is much 
more elegant.  My approach is usually to save very few frames (nstxout, etc = 
large # of steps), but certainly setting these parameters to zero is even better!



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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