Re: [gmx-users] g_h2order problem
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 InputGeneric trajectory: xtc trr trj gro g96 pdb -n order_h2o.ndx InputIndex file -nm index.ndx Input, Opt. Index file -sbso20md.tpr InputGeneric 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 -niceint 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 boolyes 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. -slint100 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 frame1550 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
[gmx-users] g_h2order problem
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 InputGeneric trajectory: xtc trr trj gro g96 pdb -n order_h2o.ndx InputIndex file -nm index.ndx Input, Opt. Index file -sbso20md.tpr InputGeneric 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 -niceint 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 boolyes 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. -slint100 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 frame1550 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
