[gmx-users] Deshuffling of .xtc file

Ivano Eberini ivano.eberini at unimi.it
Sat Nov 27 18:31:00 CET 2004

Hi all,

we run an MD simulation of a protein in water on 16 CPUs, using the 
-shuffle -sort options.
Now we need to deshuffle our .trr and .xtc files. We used the index 
deshuf.ndx file and it worked on the .trr file:
trjconv -f traj.trr -n deshuf -o deshuf.trr

but not on the .xtc file:
trjconv -f traj.xtc -n deshuf -o deshuf.xtc

The command exited with the following output:

Will write xtc: Compressed trajectory (portable xdr format)
Select group for output
Group     0 (   DeShuffle) has 54039 elements
Group     1 (DeShuffle_xtc) has  1586 elements
Select a group: 1
Selected 1: 'DeShuffle_xtc'
Reading frame       0 time    0.000
Precision of 1GX9_full.xtc is 0.001 (nm)
Using output precision of 0.001 (nm)

Back Off! I just backed up deshuf.xtc to ./#deshuf.xtc.7#
Fatal error: Index[1584] 54039 is larger than the number of atoms in 
the trajectory file (1585)

Searching the mailing list, I found out some messages from David van 
der Spoel, Dallas Warren and Bert de Groot about some troubles due to a 
mixed (between the old and the new) format of the deshuf.ndx file.
So I tried to renumber (+1) the deshuf.ndx file or to change its format 
(as suggested by David), but this didn't work, yet.

Any suggestion about how to deshuffle our .xtc file?

Thanks in advance and best regards,
Ivano Eberini
Gruppo di Studio per la Proteomica e la Struttura delle Proteine
Dipartimento di Scienze Farmacologiche
Università degli Studi di Milano
Via G. Balzaretti, 9
20133 - Milano
Tel. +39-02-503-18304/-18395
Fax +39-02-503-18284

"Quelli che scavano il sole cercando un ombra migliore"

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