[gmx-users] g_h2order problem
David van der Spoel
spoel at xray.bmc.uu.se
Wed May 24 08:56:57 CEST 2006
Rongliang Wu wrote:
> Hello, gmx-users，
>
>
> my system has just 2827 water molecules, but the g_h2order command told me
> that there are more than 2807 waters in each slice. there are only one group in
> my index file and in O H H sequence. why?
this is the sum over all frames. so this is normal. do it for a single
frame to test it.
>
>
> the results are as follows:
>
> :-) G R O M A C S (-:
>
> Go Rough, Oppose Many Angry Chinese Serial killers
>
> :-) 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_h2order (-:
>
> Option Filename Type Description
> ------------------------------------------------------------
> -f 10ns.xtc Input Generic trajectory: xtc trr trj gro g96 pdb
> -n order_h2o.ndx Input Index file
> -nm index.ndx Input, Opt. Index file
> -s bso20md.tpr Input Generic run input: tpr tpb tpa xml
> -o order.xvg Output xvgr/xmgr file
>
> Option Type Value Description
> ------------------------------------------------------
> -[no]h bool no Print help info and quit
> -[no]X bool no Use dialog box GUI to edit command line options
> -nice int 19 Set the nicelevel
> -b time 2600 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 string Z Take the normal on the membrane in direction X, Y
> or Z.
> -sl int 100 Calculate order parameter as function of
> boxlength, dividing the box in #nr slices.
>
> Reading file bso20md.tpr, VERSION 3.3 (single precision)
> Group 0 ( OW_HW1_HW2) has 8481 elements
> There is one group in the index
> Reading frame 0 time 2600.000 Box divided in 100 slices. Initial width
> o
> f slice: 0.103958
> Reading frame 1550 time 9980.000
>
> Read trajectory. Printing parameters to file
> 91697 waters in slice 0
> 91534 waters in slice 1
> 91403 waters in slice 2
> 91630 waters in slice 3
> 90943 waters in slice 4
> 91577 waters in slice 5
> 91589 waters in slice 6
> 91367 waters in slice 7
> 91485 waters in slice 8
> 91641 waters in slice 9
> 91528 waters in slice 10
> 91599 waters in slice 11
> 91867 waters in slice 12
> 92253 waters in slice 13
> 92324 waters in slice 14
> 92318 waters in slice 15
> 91075 waters in slice 16
> 87944 waters in slice 17
> 82109 waters in slice 18
> 75151 waters in slice 19
> 67429 waters in slice 20
> 57285 waters in slice 21
> 42809 waters in slice 22
> 26212 waters in slice 23
> 12391 waters in slice 24
> 4453 waters in slice 25
> 1129 waters in slice 26
> 204 waters in slice 27
> 29 waters in slice 28
> 3 waters in slice 29
> 0 waters in slice 30
> No water in slice 30
> 0 waters in slice 31
> No water in slice 31
> 0 waters in slice 32
> No water in slice 32
> 0 waters in slice 33
> No water in slice 33
> 0 waters in slice 34
> No water in slice 34
> 0 waters in slice 35
> No water in slice 35
> 0 waters in slice 36
> No water in slice 36
> 0 waters in slice 37
> No water in slice 37
> 0 waters in slice 38
> No water in slice 38
> 0 waters in slice 39
> No water in slice 39
> 0 waters in slice 40
> No water in slice 40
> 0 waters in slice 41
> No water in slice 41
> 0 waters in slice 42
> No water in slice 42
> 0 waters in slice 43
> No water in slice 43
> 0 waters in slice 44
> No water in slice 44
> 0 waters in slice 45
> No water in slice 45
> 0 waters in slice 46
> No water in slice 46
> 0 waters in slice 47
> No water in slice 47
> 0 waters in slice 48
> No water in slice 48
> 0 waters in slice 49
> No water in slice 49
> 0 waters in slice 50
> No water in slice 50
> 0 waters in slice 51
> No water in slice 51
> 0 waters in slice 52
> No water in slice 52
> 0 waters in slice 53
> No water in slice 53
> 0 waters in slice 54
> No water in slice 54
> 0 waters in slice 55
> No water in slice 55
> 0 waters in slice 56
> No water in slice 56
> 0 waters in slice 57
> No water in slice 57
> 0 waters in slice 58
> No water in slice 58
> 0 waters in slice 59
> No water in slice 59
> 0 waters in slice 60
> No water in slice 60
> 0 waters in slice 61
> No water in slice 61
> 0 waters in slice 62
> No water in slice 62
> 1 waters in slice 63
> 0 waters in slice 64
> No water in slice 64
> 1 waters in slice 65
> 1 waters in slice 66
> 17 waters in slice 67
> 146 waters in slice 68
> 927 waters in slice 69
> 3949 waters in slice 70
> 11786 waters in slice 71
> 25972 waters in slice 72
> 43494 waters in slice 73
> 58953 waters in slice 74
> 67984 waters in slice 75
> 75606 waters in slice 76
> 82786 waters in slice 77
> 88528 waters in slice 78
> 91561 waters in slice 79
> 92741 waters in slice 80
> 92275 waters in slice 81
> 92023 waters in slice 82
> 91709 waters in slice 83
> 91688 waters in slice 84
> 91710 waters in slice 85
> 91667 waters in slice 86
> 91272 waters in slice 87
> 91625 waters in slice 88
> 91645 waters in slice 89
> 91193 waters in slice 90
> 91293 waters in slice 91
> 91875 waters in slice 92
> 91003 waters in slice 93
> 91650 waters in slice 94
> 91379 waters in slice 95
> 91366 waters in slice 96
> 91429 waters in slice 97
> 91357 waters in slice 98
> 91222 waters in slice 99
> 100 slices
>
> Back Off! I just backed up order.xvg to ./#order.xvg.6#
>
> gcq#215: "I've Got Two Turntables and a Microphone" (B. Hansen)
>
>
>
>
> Regards
>
> Thanks
>
>
> Rongliang Wu
> wurl04 at iccas.ac.cn
> 2006-05-24
>
>
> ------------------------------------------------------------------------
>
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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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