[gmx-users] trjconv -split

Mark Abraham mark.j.abraham at gmail.com
Thu Dec 13 19:32:10 CET 2012


That shouldn't happen - looks like a memory problem. There's no value to
you here in running in double precision - does the problem occur with
single-precision trjconv?

Mark

On Thu, Dec 13, 2012 at 4:47 PM, Wall, Michael E <mewall at lanl.gov> wrote:

> possible bug in trjconv -split.
>
> I'm using the following command to export a set of .pdb files from a .xtc
> trajectory:
>
> trjconv_d -f md_0_1_solv.xtc -o md_0_1_solv_.pdb -s md_0_1_solv.tpr -split
> 500
>
> After writing the 250th file, gromacs quits with the below error message.
> By contrast, gromacs completes the full export using -split 5000 instead of
> -split 500, in which case the total number of files is <250.
>
>
>
> Cheers,
>
> Mike
>
> ---
>
> Error message:
>
>  ->  frame  62750 time 125500.000        ->  frame  62000 time 124000.000
> -------------------------------------------------------
> Program trjconv_d, VERSION 4.5.5
> Source code file: futil.c, line: 905
>
> Fatal error:
> Library file residuetypes.dat not found in current dir nor in default
> directories.
> (You can set the directories to search with the GMXLIB path variable)
> For more information and tips for troubleshooting, please check the GROMACS
> website at http://www.gromacs.org/Documentation/Errors
> -------------------------------------------------------
>
> Full output:
>
>
>                          :-)  G  R  O  M  A  C  S  (-:
>
>            Glycine aRginine prOline Methionine Alanine Cystine Serine
>
>                             :-)  VERSION 4.5.5  (-:
>
>         Written by Emile Apol, Rossen Apostolov, Herman J.C. Berendsen,
>       Aldert van Buuren, Pär Bjelkmar, Rudi van Drunen, Anton Feenstra,
>         Gerrit Groenhof, Peter Kasson, Per Larsson, Pieter Meulenhoff,
>            Teemu Murtola, Szilard Pall, Sander Pronk, Roland Schulz,
>                 Michael Shirts, Alfons Sijbers, Peter Tieleman,
>
>                Berk Hess, David van der Spoel, and Erik Lindahl.
>
>        Copyright (c) 1991-2000, University of Groningen, The Netherlands.
>             Copyright (c) 2001-2010, The GROMACS development team at
>         Uppsala University & The Royal Institute of Technology, Sweden.
>             check out http://www.gromacs.org for more information.
>
>          This program is free software; you can redistribute it and/or
>           modify it under the terms of the GNU General Public License
>          as published by the Free Software Foundation; either version 2
>              of the License, or (at your option) any later version.
>
>                      :-)  trjconv_d (double precision)  (-:
>
> Option     Filename  Type         Description
> ------------------------------------------------------------
>   -f md_0_1_solv.xtc  Input        Trajectory: xtc trr trj gro g96 pdb cpt
>   -o md_0_1_solv_.pdb  Output       Trajectory: xtc trr trj gro g96 pdb
>   -s md_0_1_solv.tpr  Input, Opt!  Structure+mass(db): tpr tpb tpa gro g96
> pdb
>   -n      index.ndx  Input, Opt.  Index file
>  -fr     frames.ndx  Input, Opt.  Index file
> -sub    cluster.ndx  Input, Opt.  Index file
> -drop      drop.xvg  Input, Opt.  xvgr/xmgr file
>
> Option       Type   Value   Description
> ------------------------------------------------------
> -[no]h       bool   no      Print help info and quit
> -[no]version bool   no      Print version info and quit
> -nice        int    19      Set the nicelevel
> -b           time   0       First frame (ps) to read from trajectory
> -e           time   0       Last frame (ps) to read from trajectory
> -tu          enum   ps      Time unit: fs, ps, ns, us, ms or s
> -[no]w       bool   no      View output .xvg, .xpm, .eps and .pdb files
> -xvg         enum   xmgrace  xvg plot formatting: xmgrace, xmgr or none
> -skip        int    1       Only write every nr-th frame
> -dt          time   0       Only write frame when t MOD dt = first time
> (ps)
> -[no]round   bool   no      Round measurements to nearest picosecond
> -dump        time   -1      Dump frame nearest specified time (ps)
> -t0          time   0       Starting time (ps) (default: don't change)
> -timestep    time   0       Change time step between input frames (ps)
> -pbc         enum   none    PBC treatment (see help text for full
>                             description): none, mol, res, atom, nojump,
>                             cluster or whole
> -ur          enum   rect    Unit-cell representation: rect, tric or compact
> -[no]center  bool   no      Center atoms in box
> -boxcenter   enum   tric    Center for -pbc and -center: tric, rect or zero
> -box         vector 0 0 0   Size for new cubic box (default: read from
> input)
> -clustercenter vector 0 0 0   Optional starting point for pbc cluster
> option
> -trans       vector 0 0 0   All coordinates will be translated by trans.
> This
>                             can advantageously be combined with -pbc mol
> -ur
>                             compact.
> -shift       vector 0 0 0   All coordinates will be shifted by
> framenr*shift
> -fit         enum   none    Fit molecule to ref structure in the structure
>                             file: none, rot+trans, rotxy+transxy,
>                             translation, transxy or progressive
> -ndec        int    3       Precision for .xtc and .gro writing in number
> of
>                             decimal places
> -[no]vel     bool   yes     Read and write velocities if possible
> -[no]force   bool   no      Read and write forces if possible
> -trunc       time   -1      Truncate input trajectory file after this time
>                             (ps)
> -exec        string         Execute command for every output frame with the
>                             frame number as argument
> -[no]app     bool   no      Append output
> -split       time   500     Start writing new file when t MOD split = first
>                             time (ps)
> -[no]sep     bool   no      Write each frame to a separate .gro, .g96 or
> .pdb
>                             file
> -nzero       int    0       If the -sep flag is set, use these many digits
>                             for the file numbers and prepend zeros as
> needed
> -dropunder   real   0       Drop all frames below this value
> -dropover    real   0       Drop all frames above this value
> -[no]conect  bool   no      Add conect records when writing .pdb files.
>                             Useful for visualization of non-standard
>                             molecules, e.g. coarse grained ones
>
> Will write pdb: Protein data bank file
> Reading file md_0_1_solv.tpr, VERSION 4.5.5 (double precision)
> Reading file md_0_1_solv.tpr, VERSION 4.5.5 (double precision)
> Select group for output
> Group     0 (         System) has  6517 elements
> Group     1 (          Water) has  6477 elements
> Group     2 (            SOL) has  6477 elements
> Group     3 (      non-Water) has    40 elements
> Group     4 (            Ion) has    40 elements
> Group     5 (             CL) has    40 elements
> Group     6 ( Water_and_ions) has  6517 elements
> Select a group: 6
> Selected 6: 'Water_and_ions'
> Reading frame       0 time    0.000
> Precision of md_0_1_solv.xtc is 0.001 (nm)
>  ->  frame  62750 time 125500.000        ->  frame  62000 time 124000.000
> -------------------------------------------------------
> Program trjconv_d, VERSION 4.5.5
> Source code file: futil.c, line: 905
>
> Fatal error:
> Library file residuetypes.dat not found in current dir nor in default
> directories.
> (You can set the directories to search with the GMXLIB path variable)
> For more information and tips for troubleshooting, please check the GROMACS
> website at http://www.gromacs.org/Documentation/Errors
> -------------------------------------------------------
>
> Thanx for Using GROMACS - Have a Nice Day
>
>
>
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