[gmx-users] Deshuffling of .xtc file
spoel at xray.bmc.uu.se
Sun Nov 28 22:27:32 CET 2004
On Sat, 2004-11-27 at 18:31 +0100, Ivano Eberini wrote:
> 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 54039 is larger than the number of atoms in
> the trajectory file (1585)
Could it be that you have only written your protein to the xtc file?
Check with gmxcheck
> 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"
> gmx-users mailing list
> gmx-users at gromacs.org
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org.
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596, 75124 Uppsala, Sweden
phone: 46 18 471 4205 fax: 46 18 511 755
spoel at xray.bmc.uu.se spoel at gromacs.org http://xray.bmc.uu.se/~spoel
More information about the gromacs.org_gmx-users