[gmx-users] 3.3.2 -b option not functioning as expected
David van der Spoel
spoel at xray.bmc.uu.se
Mon Apr 21 17:22:59 CEST 2008
Chris Neale wrote:
> Hello,
>
> I find that trjconv and g_order 3.3.2 don't properly find the frame to
> which I would like to seek via -b. I initially discovered this based on
> the output to the command line from g_order about which frame is being
> processed, and I have further confirmed that the incorrect frame is
> actually getting processed by g_order. Since I believe that the routine
> for -b is common to all programs, I tested trjconv and it shows the same
> features. The frame is seekable by trjconv -b only with 3.3 and 3.3.1,
> but not with 3.3.2. The simple workaround is to go through trjconv -b -e
> with 3.3 or 3.3.1and then run g_order 3.3.2 without -b or -e.
I think it should work in 3.3.3, if not please file a bugzilla.
>
> 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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--
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596, 75124 Uppsala, Sweden
phone: 46 18 471 4205 fax: 46 18 511 755
spoel at xray.bmc.uu.se spoel at gromacs.org http://folding.bmc.uu.se
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