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 <mew...@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@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-requ...@gromacs.org. > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- gmx-users mailing list gmx-users@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-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
