[gmx-users] trjcat crashes with error 9360 killed when concatenating large number of frames, bug ?

[Justin A. Lemkul]

maria goranovic wrote:
> I am using the command:
> 
> trjcat -f *gro -o temp.xtc -cat 
> 
> to concatenate about 40,000 frames of 14,000 atoms each. The commands 
> works well for 10,000 frames, but crashes for 40,000 frames after 
> reading all the frames. There is sufficient disk space. Is this a bug of 
> some kind? 
> 

Not a bug, but rather clunky code - trjcat consumes a huge amount of memory.  If 
your .gro files are large, then that is the likely limitation.  Convert the .gro 
frames to .xtc with trjconv, then concatenate those instead.

-Justin

> -- 
> Maria G.
> Technical University of Denmark
> Copenhagen
> 

-- 
========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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