[gmx-users] g_h2order problem

[Rongliang Wu]

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? 


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