[gmx-users] g_dist output

Justin A. Lemkul jalemkul at vt.edu
Tue Mar 9 15:08:08 CET 2010



John Shultz wrote:
> Here is what our script is doing. It looks to me like we are analyzing
> the tpr when we should be checking the xtc or trr if I understand you
> correctly. And if we look at the trajectory we can measure the drift
> for the entire simulation rather than a specific instance.

The .tpr file is required input for g_dist, but the frame(s) actually analyzed 
are in the generic trajectory file passed to the -f flag.  Both the .tpr and 
trajectory are required input.  This trajectory can be .xtc, .trr, .gro, .pdb, 
or a few others.  The program uses information about the atoms in the .tpr file 
to carry out the analysis on the trajectory.  As you've shown, you pass "md.gro" 
to g_dist, so you will only ever have that .gro file's information.  While it is 
possible to write the entire trajectory in .gro format, this is very 
inconvenient, since the file size gets large in a hurry, so I assume your 
"md.gro" is just a single frame, so you're getting exactly what you should 
expect.  If you want distances over time, pass a .xtc or .trr to the -f option 
of g_dist.

-Justin

> 
> 
> make_ndx -f md.tpr < make_ndx.txt
>                          :-)  G  R  O  M  A  C  S  (-:
> 
>                       GROup of MAchos and Cynical Suckers
> 
>                             :-)  VERSION 4.0.5  (-:
> 
> 
>       Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.
>        Copyright (c) 1991-2000, University of Groningen, The Netherlands.
>              Copyright (c) 2001-2008, 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.
> 
>                                :-)  make_ndx  (-:
> 
> Option     Filename  Type         Description
> ------------------------------------------------------------
>   -f         md.tpr  Input, Opt!  Structure file: gro g96 pdb tpr tpb tpa
>   -n      index.ndx  Input, Opt., Mult. Index file
>   -o      index.ndx  Output       Index file
> 
> Option       Type   Value   Description
> ------------------------------------------------------
> -[no]h       bool   no      Print help info and quit
> -nice        int    0       Set the nicelevel
> -natoms      int    0       set number of atoms (default: read from
>                             coordinate or index file)
> 
> Reading file md.tpr, VERSION 4.0.5 (single precision)
> 
> Reading structure file
> Reading file md.tpr, VERSION 4.0.5 (single precision)
> Going to read 0 old index file(s)
> Analysing residue names:
> Opening library file /usr/local/gromacs/share/gromacs/top/aminoacids.dat
> There are: 11489      OTHER residues
> There are:   244    PROTEIN residues
> There are:     0        DNA residues
> Analysing Protein...
> Analysing Other...
> 
>   0 System              : 38210 atoms
>   1 Protein             :  3868 atoms
>   2 Protein-H           :  1980 atoms
>   3 C-alpha             :   244 atoms
>   4 Backbone            :   732 atoms
>   5 MainChain           :   974 atoms
>   6 MainChain+Cb        :  1206 atoms
>   7 MainChain+H         :  1198 atoms
>   8 SideChain           :  2670 atoms
>   9 SideChain-H         :  1006 atoms
>  10 Prot-Masses         :  3868 atoms
>  11 Non-Protein         : 34342 atoms
>  12 LIG                 :    46 atoms
>  13 SOL                 : 34212 atoms
>  14 Na                  :    48 atoms
>  15 Cl                  :    36 atoms
>  16 Other               : 34342 atoms
> 
>  nr : group       !   'name' nr name   'splitch' nr    Enter: list groups
>  'a': atom        &   'del' nr         'splitres' nr   'l': list residues
>  't': atom type   |   'keep' nr        'splitat' nr    'h': help
>  'r': residue         'res' nr         'chain' char
>  "name": group        'case': case sensitive           'q': save and quit
> 
> Copied index group 0 'System'
> 
> Syntax error: "q "
> 
> gcq#89: "This Doesn't Suck, It's a Black Hole !" (K.A. Feenstra)
> 
> g_dist -f md.gro -s md.tpr -n index.ndx < protein_lig.txt
>                          :-)  G  R  O  M  A  C  S  (-:
> 
>                       GROup of MAchos and Cynical Suckers
> 
>                             :-)  VERSION 4.0.5  (-:
> 
> 
>       Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.
>        Copyright (c) 1991-2000, University of Groningen, The Netherlands.
>              Copyright (c) 2001-2008, 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_dist  (-:
> 
> Option     Filename  Type         Description
> ------------------------------------------------------------
>   -f         md.gro  Input        Trajectory: xtc trr trj gro g96 pdb cpt
>   -s         md.tpr  Input        Run input file: tpr tpb tpa
>   -n      index.ndx  Input, Opt!  Index file
>   -o       dist.xvg  Output, Opt. xvgr/xmgr file
>  -lt   lifetime.xvg  Output, 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   0       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]xvgr    bool   yes     Add specific codes (legends etc.) in the output
>                             xvg files for the xmgrace program
> -dist        real   0       Print all atoms in group 2 closer than dist to
>                             the center of mass of group 1
> 
> Reading file md.tpr, VERSION 4.0.5 (single precision)
> Group     0 (      System) has 38210 elements
> Group     1 (     Protein) has  3868 elements
> Group     2 (   Protein-H) has  1980 elements
> Group     3 (     C-alpha) has   244 elements
> Group     4 (    Backbone) has   732 elements
> Group     5 (   MainChain) has   974 elements
> Group     6 (MainChain+Cb) has  1206 elements
> Group     7 ( MainChain+H) has  1198 elements
> Group     8 (   SideChain) has  2670 elements
> Group     9 ( SideChain-H) has  1006 elements
> Group    10 ( Prot-Masses) has  3868 elements
> Group    11 ( Non-Protein) has 34342 elements
> Group    12 (         LIG) has    46 elements
> Group    13 (         SOL) has 34212 elements
> Group    14 (          Na) has    48 elements
> Group    15 (          Cl) has    36 elements
> Group    16 (       Other) has 34342 elements
> Select a group: Selected 1: 'Protein'
> Select a group: Selected 12: 'LIG'
> Reading frames from gro file 'Protein in water', 38210 atoms.
> Last frame          0 time    0.000
> 
> gcq#89: "This Doesn't Suck, It's a Black Hole !" (K.A. Feenstra)
> 
> 
> # This file was created Tue Mar  9 13:58:58 2010
> # by the following command:
> # g_dist -f md.gro -s md.tpr -n index.ndx
> #
> # g_dist is part of G R O M A C S:
> #
> # GROup of MAchos and Cynical Suckers
> #
> @    title "Distance"
> @    xaxis  label "Time (ps)"
> @    yaxis  label "Distance (nm)"
> @TYPE xy
> @ view 0.15, 0.15, 0.75, 0.85
> @ legend on
> @ legend box on
> @ legend loctype view
> @ legend 0.78, 0.8
> @ legend length 2
> @ s0 legend "|d|"
> @ s1 legend "d\sx\N"
> @ s2 legend "d\sy\N"
> @ s3 legend "d\sz\N"
>    0.0000000    0.1572016   -0.1153002   -0.0301313   -0.1025198
> 
> 
> On Tue, Mar 9, 2010 at 8:46 AM, Justin A. Lemkul <jalemkul at vt.edu> wrote:
>>
>> John Shultz wrote:
>>> How come time is always  0.0000000
>>>
>> You're analyzing a .gro file, so there is no time information stored.  If
>> you analyze a trajectory (i.e., .xtc or .trr), then the time is saved in the
>> individual frames.
>>
>> -Justin
>>
>>> On Tue, Mar 9, 2010 at 8:16 AM, Justin A. Lemkul <jalemkul at vt.edu> wrote:
>>>> John Shultz wrote:
>>>>> Hello,
>>>>>
>>>>> I am seeking clarification on what this output means. I believe it
>>>>> says that the x axis is divided into 4 time intervals and they are
>>>>> plotted against a y axis that measures total distance along all 3
>>>>> dimensional coordinates.
>>>>> Am I reading this correctly?
>>>>>
>>>> There should be no decomposition of time intervals here.  Distance is
>>>> plotted continuously as a function of time.  The first column is time,
>>>> then
>>>> the total distance, then each of the x, y, and z components of that
>>>> distance.
>>>>
>>>> -Justin
>>>>
>>>>> # This file was created Sat Jan 30 00:20:03 2010
>>>>> # by the following command:
>>>>> # g_dist -f md.gro -s md.tpr -n index.ndx
>>>>> #
>>>>> # g_dist is part of G R O M A C S:
>>>>> #
>>>>> # Glycine aRginine prOline Methionine Alanine Cystine Serine
>>>>> #
>>>>> @    title "Distance"
>>>>> @    xaxis  label "Time (ps)"
>>>>> @    yaxis  label "Distance (nm)"
>>>>> @TYPE xy
>>>>> @ view 0.15, 0.15, 0.75, 0.85
>>>>> @ legend on
>>>>> @ legend box on
>>>>> @ legend loctype view
>>>>> @ legend 0.78, 0.8
>>>>> @ legend length 2
>>>>> @ s0 legend "|d|"
>>>>> @ s1 legend "d\sx\N"
>>>>> @ s2 legend "d\sy\N"
>>>>> @ s3 legend "d\sz\N"
>>>>>  0.0000000    0.0619448    0.0583303    0.0099401   -0.0183282
>>>>>
>>>>>
>>>>>
>>>>>
>>>> --
>>>> ========================================
>>>>
>>>> Justin A. Lemkul
>>>> Ph.D. Candidate
>>>> ICTAS Doctoral Scholar
>>>> MILES-IGERT Trainee
>>>> Department of Biochemistry
>>>> Virginia Tech
>>>> Blacksburg, VA
>>>> jalemkul[at]vt.edu | (540) 231-9080
>>>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>>>>
>>>> ========================================
>>>> --
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>>>
>>>
>> --
>> ========================================
>>
>> Justin A. Lemkul
>> Ph.D. Candidate
>> ICTAS Doctoral Scholar
>> MILES-IGERT Trainee
>> Department of Biochemistry
>> Virginia Tech
>> Blacksburg, VA
>> jalemkul[at]vt.edu | (540) 231-9080
>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>>
>> ========================================
>> --
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> 
> 
> 

-- 
========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

========================================



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