[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
>
>
>
> --
> gmx-users mailing list gmx-users at gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> * Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org.
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
More information about the gromacs.org_gmx-users
mailing list