Perhaps I have made some mistake or perhaps this is a known problem, but
I couldn't find any mention of it.
Below is the output from my tests in case anybody can verify this.
Chris.
##############################################
The frame at 10ns is seekable by trjconv 3.3.1 but not by trjconv 3.3.2:
$ trjconv -f bilayer_popc_0-15.6ns.xtc -o a.gro -b 10000 -e 10000 -s
empty.tpr
:-) G R O M A C S (-:
Glycine aRginine prOline Methionine Alanine Cystine Serine
:-) VERSION 3.3 (-:
Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.
Copyright (c) 1991-2000, University of Groningen, The Netherlands.
Copyright (c) 2001-2004, The GROMACS development team,
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 (-:
Option Filename Type Description
------------------------------------------------------------
-f bilayer_popc_0-15.6ns.xtc Input Generic trajectory: xtc trr trj
gro g96 pdb
-o a.gro Output Generic trajectory: xtc trr trj gro g96
pdb
-s empty.tpr Input, Opt! Structure+mass(db): tpr tpb tpa gro g96
pdb
xml
-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
-nice int 19 Set the nicelevel
-b time 10000 First frame (ps) to read from trajectory
-e time 10000 Last frame (ps) to read from trajectory
-tu enum ps Time unit: ps, fs, ns, us, ms, s, m or h
-[no]w bool no View output xvg, xpm, eps and pdb files
-[no]xvgr bool yes Add specific codes (legends etc.) in the output
xvg files for the xmgrace program
-skip int 1 Only write every nr-th frame
-dt time 0 Only write frame when t MOD dt = first time (ps)
-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, whole, inbox, nojump,
cluster
or com
-ur enum rect Unit-cell representation: rect, tric or compact
-center enum no Center atoms in box: no, tric, rect or zero
-box vector 0 0 0 Size for new cubic box (default: read from
input)
-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, translation 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 trj 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 0 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
-[no]ter bool no Use 'TER' in pdb file as end of frame in
stead of
default 'ENDMDL'
-dropunder real 0 Drop all frames below this value
-dropover real 0 Drop all frames above this value
Will write gro: Coordinate file in Gromos-87 format
Reading file empty.tpr, VERSION 3.3.1 (single precision)
Reading file empty.tpr, VERSION 3.3.1 (single precision)
Select group for output
Opening library file /home/cneale/gromacs/top/aminoacids.dat
Group 0 ( System) has 70168 elements
Group 1 ( POPC) has 16640 elements
Group 2 ( SOL) has 53528 elements
Select a group: 0
Selected 0: 'System'
Reading frame 0 time 10000.000 Precision of
bilayer_popc_0-15.6ns.xtc is 0.001 (nm)
Using output precision of 0.001 (nm)
Last frame 0 time 10000.000
gcq#150: "Carry Me Away" (Motors)
###############
$trjconv -f bilayer_popc_0-15.6ns.xtc -o a.gro -b 10000 -e 10000 -s
empty.tpr
:-) G R O M A C S (-:
GROningen Mixture of Alchemy and Childrens' Stories
:-) VERSION 3.3.1 (-:
Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.
Copyright (c) 1991-2000, University of Groningen, The Netherlands.
Copyright (c) 2001-2006, The GROMACS development team,
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 (-:
Option Filename Type Description
------------------------------------------------------------
-f bilayer_popc_0-15.6ns.xtc Input Generic trajectory: xtc trr trj
gro g96 pdb
-o a.gro Output Generic trajectory: xtc trr trj gro g96
pdb
-s empty.tpr Input, Opt! Structure+mass(db): tpr tpb tpa gro g96
pdb
xml
-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
-nice int 19 Set the nicelevel
-b time 10000 First frame (ps) to read from trajectory
-e time 10000 Last frame (ps) to read from trajectory
-tu enum ps Time unit: ps, fs, ns, us, ms or s
-[no]w bool no View output xvg, xpm, eps and pdb files
-[no]xvgr bool yes Add specific codes (legends etc.) in the output
xvg files for the xmgrace program
-skip int 1 Only write every nr-th frame
-dt time 0 Only write frame when t MOD dt = first time (ps)
-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, whole, inbox, nojump,
cluster
or com
-ur enum rect Unit-cell representation: rect, tric or compact
-center enum no Center atoms in box: no, tric, rect or zero
-box vector 0 0 0 Size for new cubic box (default: read from
input)
-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, translation 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 trj 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 0 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
-[no]ter bool no Use 'TER' in pdb file as end of frame in
stead of
default 'ENDMDL'
-dropunder real 0 Drop all frames below this value
-dropover real 0 Drop all frames above this value
Will write gro: Coordinate file in Gromos-87 format
Reading file empty.tpr, VERSION 3.3.1 (single precision)
Reading file empty.tpr, VERSION 3.3.1 (single precision)
Select group for output
Opening library file /home/cneale/gromacs/top/aminoacids.dat
Group 0 ( System) has 70168 elements
Group 1 ( POPC) has 16640 elements
Group 2 ( SOL) has 53528 elements
Select a group: 0
Selected 0: 'System'
Reading frame 0 time 10000.000 Precision of
bilayer_popc_0-15.6ns.xtc is 0.001 (nm)
Using output precision of 0.001 (nm)
Last frame 0 time 10000.000
######################
$/hpf/data/pomes/cneale/exe/gromacs-3.3.2/exec/bin/trjconv -f
bilayer_popc_0-15.6ns.xtc -o a.gro -b 10000 -e 10000 -s empty.tpr
:-) G R O M A C S (-:
Glycine aRginine prOline Methionine Alanine Cystine Serine
:-) VERSION 3.3.2 (-:
Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.
Copyright (c) 1991-2000, University of Groningen, The Netherlands.
Copyright (c) 2001-2007, The GROMACS development team,
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.
:-) /hpf/data/pomes/cneale/exe/gromacs-3.3.2/exec/bin/trjconv (-:
Option Filename Type Description
------------------------------------------------------------
-f bilayer_popc_0-15.6ns.xtc Input Generic trajectory: xtc trr trj
gro g96 pdb
-o a.gro Output Generic trajectory: xtc trr trj gro g96
pdb
-s empty.tpr Input, Opt! Structure+mass(db): tpr tpb tpa gro g96
pdb
xml
-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
-nice int 19 Set the nicelevel
-b time 10000 First frame (ps) to read from trajectory
-e time 10000 Last frame (ps) to read from trajectory
-tu enum ps Time unit: ps, fs, ns, us, ms or s
-[no]w bool no View output xvg, xpm, eps and pdb files
-[no]xvgr bool yes Add specific codes (legends etc.) in the output
xvg files for the xmgrace program
-skip int 1 Only write every nr-th frame
-dt time 0 Only write frame when t MOD dt = first time
(ps)
-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)
-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, translation 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 trj 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 0 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
-[no]ter bool no Use 'TER' in pdb file as end of frame in
stead of
default 'ENDMDL'
-dropunder real 0 Drop all frames below this value
-dropover real 0 Drop all frames above this value
Will write gro: Coordinate file in Gromos-87 format
Reading file empty.tpr, VERSION 3.3.1 (single precision)
Reading file empty.tpr, VERSION 3.3.1 (single precision)
Select group for output
Opening library file /home/cneale/gromacs/top/aminoacids.dat
Group 0 ( System) has 70168 elements
Group 1 ( POPC) has 16640 elements
Group 2 ( SOL) has 53528 elements
Select a group: 0
Selected 0: 'System'
Last frame -1 time 0.000
Precision of bilayer_popc_0-15.6ns.xtc is 0.001 (nm)
Using output precision of 0.001 (nm)
WARNING no output, trajectory ended at 11710
gcq#153: "It Doesn't Have to Be Tip Top" (Pulp Fiction)
#####################################################################
g_order 3.3.2 appears to find the wrong frame, g_order 3.3.1 is broken
(known problem) and g_order 3.3 works fine
$/hpf/data/pomes/cneale/exe/gromacs-3.3.2/exec/bin/g_order -f
bilayer_popc_0-15.6ns.xtc -b 10000 -e 10000 -s empty.tpr -n
palmitoyl.ndx -od palmitoylDOP_10-15.6ns.xvg
:-) G R O M A C S (-:
GRowing Old MAkes el Chrono Sweat
:-) VERSION 3.3.2 (-:
Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.
Copyright (c) 1991-2000, University of Groningen, The Netherlands.
Copyright (c) 2001-2007, The GROMACS development team,
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.
:-) /hpf/data/pomes/cneale/exe/gromacs-3.3.2/exec/bin/g_order (-:
Option Filename Type Description
------------------------------------------------------------
-f bilayer_popc_0-15.6ns.xtc Input Generic trajectory: xtc trr trj
gro g96 pdb
-n palmitoyl.ndx Input Index file
-s empty.tpr Input Generic run input: tpr tpb tpa xml
-o order.xvg Output xvgr/xmgr file
-od palmitoylDOP_10-15.6ns.xvg Output xvgr/xmgr file
-os sliced.xvg Output xvgr/xmgr file
-Sg sg-ang.xvg Output xvgr/xmgr file
-Sk sk-dist.xvg Output xvgr/xmgr file
Option Type Value Description
------------------------------------------------------
-[no]h bool no Print help info and quit
-nice int 19 Set the nicelevel
-b time 10000 First frame (ps) to read from trajectory
-e time 10000 Last frame (ps) to read from trajectory
-dt time 0 Only use frame when t MOD dt = first time (ps)
-[no]w bool no View output xvg, xpm, eps and pdb files
-[no]xvgr bool yes Add specific codes (legends etc.) in the output
xvg files for the xmgrace program
-d enum z Direction of the normal on the membrane: z,
x or y
-sl int 1 Calculate order parameter as function of
boxlength, dividing the box in #nr slices.
-[no]szonly bool no Only give Sz element of order tensor. (axis can
be specified with -d)
-[no]unsat bool no Calculate order parameters for unsaturated
carbons. Note that this cannot be mixed with
normal order parameters.
Taking z axis as normal to the membrane
Reading file empty.tpr, VERSION 3.3.1 (single precision)
Using following groups:
Groupname: C15 First atomname: C15 First atomnr 14
Groupname: C17 First atomname: C17 First atomnr 16
Groupname: C18 First atomname: C18 First atomnr 17
Groupname: C19 First atomname: C19 First atomnr 18
Groupname: C20 First atomname: C20 First atomnr 19
Groupname: C21 First atomname: C21 First atomnr 20
Groupname: C22 First atomname: C22 First atomnr 21
Groupname: C23 First atomname: C23 First atomnr 22
Groupname: C24 First atomname: C24 First atomnr 23
Groupname: C25 First atomname: C25 First atomnr 24
Groupname: C26 First atomname: C26 First atomnr 25
Groupname: C27 First atomname: C27 First atomnr 26
Groupname: C28 First atomname: C28 First atomnr 27
Groupname: C29 First atomname: C29 First atomnr 28
Groupname: C30 First atomname: C30 First atomnr 29
Groupname: C31 First atomname: C31 First atomnr 30
Groupname: CA1 First atomname: CA1 First atomnr 50
Groupname: CA2 First atomname: CA2 First atomnr 51
Last frame -1 time 0.000 Number of elements in first group:
320
Last frame -1 time 11710.000
Read trajectory. Printing parameters to file
Atom 1 Tensor: x=-0.147642 , y=-0.171352, z=0.318993
Atom 2 Tensor: x=-0.188145 , y=-0.160864, z=0.349009
Atom 3 Tensor: x=-0.207471 , y=-0.18523, z=0.392701
Atom 4 Tensor: x=-0.225034 , y=-0.197889, z=0.422923
Atom 5 Tensor: x=-0.230958 , y=-0.160066, z=0.391024
Atom 6 Tensor: x=-0.24148 , y=-0.15959, z=0.401069
Atom 7 Tensor: x=-0.229353 , y=-0.10434, z=0.333693
Atom 8 Tensor: x=-0.224349 , y=-0.075672, z=0.300021
Atom 9 Tensor: x=-0.217044 , y=0.0937857, z=0.123259
Atom 10 Tensor: x=-0.185461 , y=0.00712792, z=0.178333
Atom 11 Tensor: x=-0.196563 , y=-0.0723973, z=0.26896
Atom 12 Tensor: x=-0.144809 , y=-0.0295547, z=0.174363
Atom 13 Tensor: x=-0.153018 , y=-0.0276582, z=0.180677
Atom 14 Tensor: x=-0.111531 , y=-0.042281, z=0.153812
Atom 15 Tensor: x=-0.123816 , y=-0.022849, z=0.146665
Atom 16 Tensor: x=-0.0667708 , y=-0.0103386, z=0.0771094
gcq#34: "Sisters Have Always Fascinated Me" (Speech)
#############
Using gromacs 3.3 the correct frame is found when using -b option to
g_order
$ g_order -s empty.tpr -f bilayer_popc_0-15.6ns.xtc -b 10000 -n
palmitoyl.ndx -od
:-) G R O M A C S (-:
Giant Rising Ordinary Mutants for A Clerical Setup
:-) VERSION 3.3 (-:
Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.
Copyright (c) 1991-2000, University of Groningen, The Netherlands.
Copyright (c) 2001-2004, The GROMACS development team,
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.
:-) g_order (-:
Option Filename Type Description
------------------------------------------------------------
-f bilayer_popc_0-15.6ns.xtc Input Generic trajectory: xtc trr trj
gro g96 pdb
-n palmitoyl.ndx Input Index file
-s empty.tpr Input Generic run input: tpr tpb tpa xml
-o order.xvg Output xvgr/xmgr file
-od deuter.xvg Output xvgr/xmgr file
-os sliced.xvg Output xvgr/xmgr file
Option Type Value Description
------------------------------------------------------
-[no]h bool no Print help info and quit
-nice int 19 Set the nicelevel
-b time 10000 First frame (ps) to read from trajectory
-e time 0 Last frame (ps) to read from trajectory
-dt time 0 Only use frame when t MOD dt = first time (ps)
-[no]w bool no View output xvg, xpm, eps and pdb files
-[no]xvgr bool yes Add specific codes (legends etc.) in the output
xvg files for the xmgrace program
-d enum z Direction of the normal on the membrane: z, x or
y
-sl int 1 Calculate order parameter as function of
boxlength, dividing the box in #nr slices.
-[no]szonly bool no Only give Sz element of order tensor. (axis can
be specified with -d)
-[no]unsat bool no Calculate order parameters for unsaturated
carbons. Note that this cannot be mixed with
normal order parameters.
Taking z axis as normal to the membrane
Reading file empty.tpr, VERSION 3.3.1 (single precision)
Using following groups:
Groupname: C15 First atomname: C15 First atomnr 14
Groupname: C17 First atomname: C17 First atomnr 16
Groupname: C18 First atomname: C18 First atomnr 17
Groupname: C19 First atomname: C19 First atomnr 18
Groupname: C20 First atomname: C20 First atomnr 19
Groupname: C21 First atomname: C21 First atomnr 20
Groupname: C22 First atomname: C22 First atomnr 21
Groupname: C23 First atomname: C23 First atomnr 22
Groupname: C24 First atomname: C24 First atomnr 23
Groupname: C25 First atomname: C25 First atomnr 24
Groupname: C26 First atomname: C26 First atomnr 25
Groupname: C27 First atomname: C27 First atomnr 26
Groupname: C28 First atomname: C28 First atomnr 27
Groupname: C29 First atomname: C29 First atomnr 28
Groupname: C30 First atomname: C30 First atomnr 29
Groupname: C31 First atomname: C31 First atomnr 30
Groupname: CA1 First atomname: CA1 First atomnr 50
Groupname: CA2 First atomname: CA2 First atomnr 51
Reading frame 0 time 10000.000 Number of elements in first
group: 320
Last frame 560 time 15600.000
Read trajectory. Printing parameters to file
Atom 1 Tensor: x=-0.163387 , y=-0.173428, z=0.336815
Atom 2 Tensor: x=-0.19414 , y=-0.165269, z=0.359409
Atom 3 Tensor: x=-0.187481 , y=-0.187444, z=0.374925
Atom 4 Tensor: x=-0.210546 , y=-0.173912, z=0.384458
Atom 5 Tensor: x=-0.20022 , y=-0.160333, z=0.360553
Atom 6 Tensor: x=-0.219888 , y=-0.164878, z=0.384767
Atom 7 Tensor: x=-0.202653 , y=-0.106491, z=0.309144
Atom 8 Tensor: x=-0.218463 , y=-0.0580569, z=0.27652
Atom 9 Tensor: x=-0.218421 , y=0.0399221, z=0.178499
Atom 10 Tensor: x=-0.197942 , y=-0.0241576, z=0.2221
Atom 11 Tensor: x=-0.204984 , y=-0.0886371, z=0.293621
Atom 12 Tensor: x=-0.155557 , y=-0.0858337, z=0.241391
Atom 13 Tensor: x=-0.163629 , y=-0.0933451, z=0.256974
Atom 14 Tensor: x=-0.122696 , y=-0.0822174, z=0.204913
Atom 15 Tensor: x=-0.124952 , y=-0.0694788, z=0.194431
Atom 16 Tensor: x=-0.0778629 , y=-0.0536229, z=0.131486
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