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Hi,<br><br>This is a bug caused by last minute additions of some stuff to the checkpoint file.<br>I have fixed it for 4.0.1.<br><br>Berk<br><br>> Date: Wed, 5 Nov 2008 22:24:15 -0500<br>> From: chris.neale@utoronto.ca<br>> To: gmx-users@gromacs.org<br>> Subject: [gmx-users] trjconv -f .cpt -s .tpr -o .gro<br>> <br>> Hello,<br>> <br>> has anybody successfully used trjconv to obtain a .gro file from a <br>> .cpt file in gromacs 4.0?<br>> <br>> Thanks,<br>> Chris.<br>> <br>> [cneale@rb17 16core]$ /work/cneale/exe/gromacs-4.0/exec/bin/trjconv -f <br>> test.xtc -s test.tpr -o my.gro<br>> :-) G R O M A C S (-:<br>> <br>> Getting the Right Output Means no Artefacts in Calculating Stuff<br>> <br>> :-) VERSION 4.0 (-:<br>> <br>> <br>> Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.<br>> Copyright (c) 1991-2000, University of Groningen, The Netherlands.<br>> Copyright (c) 2001-2008, The GROMACS development team,<br>> check out http://www.gromacs.org for more information.<br>> <br>> This program is free software; you can redistribute it and/or<br>> modify it under the terms of the GNU General Public License<br>> as published by the Free Software Foundation; either version 2<br>> of the License, or (at your option) any later version.<br>> <br>> :-) /work/cneale/exe/gromacs-4.0/exec/bin/trjconv (-:<br>> <br>> Option Filename Type Description<br>> ------------------------------------------------------------<br>> -f test.xtc Input Trajectory: xtc trr trj gro g96 pdb cpt<br>> -o my.gro Output Trajectory: xtc trr trj gro g96 pdb<br>> -s test.tpr Input, Opt! Structure+mass(db): tpr tpb tpa gro g96 pdb<br>> -n index.ndx Input, Opt. Index file<br>> -fr frames.ndx Input, Opt. Index file<br>> -sub cluster.ndx Input, Opt. Index file<br>> -drop drop.xvg Input, Opt. xvgr/xmgr file<br>> <br>> Option Type Value Description<br>> ------------------------------------------------------<br>> -[no]h bool no Print help info and quit<br>> -nice int 19 Set the nicelevel<br>> -b time 0 First frame (ps) to read from trajectory<br>> -e time 0 Last frame (ps) to read from trajectory<br>> -tu enum ps Time unit: ps, fs, ns, us, ms or s<br>> -[no]w bool no View output xvg, xpm, eps and pdb files<br>> -[no]xvgr bool yes Add specific codes (legends etc.) in the output<br>> xvg files for the xmgrace program<br>> -skip int 1 Only write every nr-th frame<br>> -dt time 0 Only write frame when t MOD dt = first time (ps)<br>> -dump time -1 Dump frame nearest specified time (ps)<br>> -t0 time 0 Starting time (ps) (default: don't change)<br>> -timestep time 0 Change time step between input frames (ps)<br>> -pbc enum none PBC treatment (see help text for full<br>> description): none, mol, res, atom, nojump,<br>> cluster or whole<br>> -ur enum rect Unit-cell representation: rect, tric or compact<br>> -[no]center bool no Center atoms in box<br>> -boxcenter enum tric Center for -pbc and -center: tric, rect or zero<br>> -box vector 0 0 0 Size for new cubic box (default: read from input)<br>> -trans vector 0 0 0 All coordinates will be translated by trans. This<br>> can advantageously be combined with -pbc mol -ur<br>> compact.<br>> -shift vector 0 0 0 All coordinates will be shifted by framenr*shift<br>> -fit enum none Fit molecule to ref structure in the structure<br>> file: none, rot+trans, rotxy+transxy, translation<br>> or progressive<br>> -ndec int 3 Precision for .xtc and .gro writing in number of<br>> decimal places<br>> -[no]vel bool yes Read and write velocities if possible<br>> -[no]force bool no Read and write forces if possible<br>> -trunc time -1 Truncate input trj file after this time (ps)<br>> -exec string Execute command for every output frame with the<br>> frame number as argument<br>> -[no]app bool no Append output<br>> -split time 0 Start writing new file when t MOD split = first<br>> time (ps)<br>> -[no]sep bool no Write each frame to a separate .gro, .g96 or .pdb<br>> file<br>> -nzero int 0 Prepend file number in case you use the -sep flag<br>> with this number of zeroes<br>> -[no]ter bool no Use 'TER' in pdb file as end of frame in stead of<br>> default 'ENDMDL'<br>> -dropunder real 0 Drop all frames below this value<br>> -dropover real 0 Drop all frames above this value<br>> <br>> Will write gro: Coordinate file in Gromos-87 format<br>> Reading file test.tpr, VERSION 4.0 (single precision)<br>> Reading file test.tpr, VERSION 4.0 (single precision)<br>> Select group for output<br>> Opening library file /home/cneale/gromacs/top/aminoacids.dat<br>> Group 0 ( System) has 59152 elements<br>> Group 1 ( Protein) has 5060 elements<br>> Group 2 ( Protein-H) has 2636 elements<br>> Group 3 ( C-alpha) has 314 elements<br>> Group 4 ( Backbone) has 942 elements<br>> Group 5 ( MainChain) has 1258 elements<br>> Group 6 (MainChain+Cb) has 1542 elements<br>> Group 7 ( MainChain+H) has 1556 elements<br>> Group 8 ( SideChain) has 3504 elements<br>> Group 9 ( SideChain-H) has 1378 elements<br>> Group 10 ( Prot-Masses) has 5060 elements<br>> Group 11 ( Non-Protein) has 54092 elements<br>> Group 12 ( POPC) has 13728 elements<br>> Group 13 ( SOL) has 40360 elements<br>> Group 14 ( NA+) has 4 elements<br>> Group 15 ( Other) has 54092 elements<br>> Select a group: 0<br>> Selected 0: 'System'<br>> Reading frame 0 time 1400.000<br>> Precision of test.xtc is 0.001 (nm)<br>> Using output precision of 0.001 (nm)<br>> Reading frame 7 time 1470.000 -> frame 7 time 1470.000<br>> [cneale@rb17 16core]$ /work/cneale/exe/gromacs-4.0/exec/bin/trjconv -f <br>> test.cpt -s test.tpr -o my.gro<br>> :-) G R O M A C S (-:<br>> <br>> S C A M O R G<br>> <br>> :-) VERSION 4.0 (-:<br>> <br>> <br>> Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.<br>> Copyright (c) 1991-2000, University of Groningen, The Netherlands.<br>> Copyright (c) 2001-2008, The GROMACS development team,<br>> check out http://www.gromacs.org for more information.<br>> <br>> This program is free software; you can redistribute it and/or<br>> modify it under the terms of the GNU General Public License<br>> as published by the Free Software Foundation; either version 2<br>> of the License, or (at your option) any later version.<br>> <br>> :-) /work/cneale/exe/gromacs-4.0/exec/bin/trjconv (-:<br>> <br>> Option Filename Type Description<br>> ------------------------------------------------------------<br>> -f test.cpt Input Trajectory: xtc trr trj gro g96 pdb cpt<br>> -o my.gro Output Trajectory: xtc trr trj gro g96 pdb<br>> -s test.tpr Input, Opt! Structure+mass(db): tpr tpb tpa gro g96 pdb<br>> -n index.ndx Input, Opt. Index file<br>> -fr frames.ndx Input, Opt. Index file<br>> -sub cluster.ndx Input, Opt. Index file<br>> -drop drop.xvg Input, Opt. xvgr/xmgr file<br>> <br>> Option Type Value Description<br>> ------------------------------------------------------<br>> -[no]h bool no Print help info and quit<br>> -nice int 19 Set the nicelevel<br>> -b time 0 First frame (ps) to read from trajectory<br>> -e time 0 Last frame (ps) to read from trajectory<br>> -tu enum ps Time unit: ps, fs, ns, us, ms or s<br>> -[no]w bool no View output xvg, xpm, eps and pdb files<br>> -[no]xvgr bool yes Add specific codes (legends etc.) in the output<br>> xvg files for the xmgrace program<br>> -skip int 1 Only write every nr-th frame<br>> -dt time 0 Only write frame when t MOD dt = first time (ps)<br>> -dump time -1 Dump frame nearest specified time (ps)<br>> -t0 time 0 Starting time (ps) (default: don't change)<br>> -timestep time 0 Change time step between input frames (ps)<br>> -pbc enum none PBC treatment (see help text for full<br>> description): none, mol, res, atom, nojump,<br>> cluster or whole<br>> -ur enum rect Unit-cell representation: rect, tric or compact<br>> -[no]center bool no Center atoms in box<br>> -boxcenter enum tric Center for -pbc and -center: tric, rect or zero<br>> -box vector 0 0 0 Size for new cubic box (default: read from input)<br>> -trans vector 0 0 0 All coordinates will be translated by trans. This<br>> can advantageously be combined with -pbc mol -ur<br>> compact.<br>> -shift vector 0 0 0 All coordinates will be shifted by framenr*shift<br>> -fit enum none Fit molecule to ref structure in the structure<br>> file: none, rot+trans, rotxy+transxy, translation<br>> or progressive<br>> -ndec int 3 Precision for .xtc and .gro writing in number of<br>> decimal places<br>> -[no]vel bool yes Read and write velocities if possible<br>> -[no]force bool no Read and write forces if possible<br>> -trunc time -1 Truncate input trj file after this time (ps)<br>> -exec string Execute command for every output frame with the<br>> frame number as argument<br>> -[no]app bool no Append output<br>> -split time 0 Start writing new file when t MOD split = first<br>> time (ps)<br>> -[no]sep bool no Write each frame to a separate .gro, .g96 or .pdb<br>> file<br>> -nzero int 0 Prepend file number in case you use the -sep flag<br>> with this number of zeroes<br>> -[no]ter bool no Use 'TER' in pdb file as end of frame in stead of<br>> default 'ENDMDL'<br>> -dropunder real 0 Drop all frames below this value<br>> -dropover real 0 Drop all frames above this value<br>> <br>> Will write gro: Coordinate file in Gromos-87 format<br>> Reading file test.tpr, VERSION 4.0 (single precision)<br>> Reading file test.tpr, VERSION 4.0 (single precision)<br>> Select group for output<br>> Opening library file /home/cneale/gromacs/top/aminoacids.dat<br>> Group 0 ( System) has 59152 elements<br>> Group 1 ( Protein) has 5060 elements<br>> Group 2 ( Protein-H) has 2636 elements<br>> Group 3 ( C-alpha) has 314 elements<br>> Group 4 ( Backbone) has 942 elements<br>> Group 5 ( MainChain) has 1258 elements<br>> Group 6 (MainChain+Cb) has 1542 elements<br>> Group 7 ( MainChain+H) has 1556 elements<br>> Group 8 ( SideChain) has 3504 elements<br>> Group 9 ( SideChain-H) has 1378 elements<br>> Group 10 ( Prot-Masses) has 5060 elements<br>> Group 11 ( Non-Protein) has 54092 elements<br>> Group 12 ( POPC) has 13728 elements<br>> Group 13 ( SOL) has 40360 elements<br>> Group 14 ( NA+) has 4 elements<br>> Group 15 ( Other) has 54092 elements<br>> Select a group: 0<br>> Selected 0: 'System'<br>> Segmentation fault<br>> <br>> <br>> _______________________________________________<br>> gmx-users mailing list gmx-users@gromacs.org<br>> http://www.gromacs.org/mailman/listinfo/gmx-users<br>> Please search the archive at http://www.gromacs.org/search before posting!<br>> Please don't post (un)subscribe requests to the list. 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